Similar to his storytelling style in his Cree Indian tales, Kinsella in Shoeless Joe suggests that the world is undergoing swift changes, often leading to the loss of invaluable treasures and resources. For instance, in the novel's storyline, Ray Kinsella's modest farm in Iowa is under the threat of being overtaken by a large computer-farming corporation, a fate that has already befallen other local farms. The novel also subtly critiques academia, religion, and "all the forces that control our lives." Despite these themes, Shoeless Joe remains primarily a captivating story. As Kinsella himself explains: "I am an old-fashioned storyteller. I try to make people laugh and cry. A fiction writer's duty is to entertain. If you then sneak in something profound or symbolic, so much the better."

Kinsella suggests that Shoeless Joe is not just a tale about baseball but rather explores the "power of love in all directions." This theme is demonstrated through the protagonist, Ray Kinsella, who shares the loves of his life: his wife Annie, his daughter Karin, Iowa, and the "great god Baseball." A fictionalized version of J.D. Salinger, the author of The Catcher in the Rye (1951), is portrayed as a fervent baseball fan. The universal love for baseball is represented by the old-time players who have passed away yet miraculously return to play on Ray's field, each with a profound passion for the game itself.

Shoeless Joe is rich with references and allusions to religious beliefs and customs. Kinsella contrasts traditional Christianity with what he sees as a more authentic, life-enhancing form of spirituality, represented by baseball. Traditional religion is portrayed unfavorably, particularly through Ray's perspective on his wife's family. Annie's mother is shown as self-righteous and judgmental, frequently inserting her religious views into discussions. Ray's brother-in-law, Mark, is a fundamentalist Christian with disdain for atheists and Catholics. Mark's three brothers are named Matthew, Luke, and John, mirroring the evangelists who wrote the four gospels, underscoring Ray's conflict with Christianity. Furthermore, Eddie Scissons's three daughters are depicted as stern, unimaginative, and joyless, reinforcing this negative portrayal.

In contrast, baseball is presented as a kind of pseudo-religion. Ray describes baseball fans as "not just ordinary people, we're a congregation." He views a ballpark at night as "more like a church than a church." Ray imagines fans waiting for a game to start, sitting "in silence, in awe, in wonder, in anticipation, in joy," akin to worshippers in a cathedral. This sense of joy is noticeably absent in Ray's view of how Christianity is generally practiced.

Baseball provides the peace and consistency that people often seek in religion. It is comforting because "it is stable and permanent." Observing Boston's Fenway Park, Ray notes that "the year might be 1900 or 1920 or 1979, for all the field itself has changed. Here the sense of urgency that governs most lives is pushed to one side." Like religion, baseball offers the possibility of miraculous events that can transcend or reverse time. Ray believes that during a baseball game, anything is possible: "Tides can reverse; oceans can open." This idea is embodied in Ray's magical baseball park, where his deep love for the game allows the dead to live again—a promise also made by traditional Christianity to its followers.

Shoeless Joe is a fantasy novel where the deceased are brought back to life, dreams materialize, and past wounds heal. The narrative highlights the value of imagination over mundane reality. For example, Ray overlooks his mounting debts, and to everyone except his supportive wife Annie, he seems doomed to fail, with selling the farm appearing to be the only logical option. However, Ray is anything but practical. He is resolute in his quest to chase his dreams and turn them into reality. To achieve this, he must remain in tune with his intuition and emotions, even if it means engaging in seemingly irrational actions, like driving across the country to take a reclusive writer to a baseball game. Ray must stay focused on his objective, ignore well-intentioned advice, and have faith in his vision. He also has to commit to hard physical work to convert his cornfield into a baseball field. This involves planting, watering, sanding, and raking the field, which symbolizes nurturing his own imagination and allowing his hidden aspirations to surface. By exploring deep within his consciousness, Ray identifies what requires healing within himself and others. He connects to a universal level of existence where all things are interconnected. From this perspective, he can help complete the "cosmic jigsaw puzzle," where everything finds its rightful place and time. As long as Ray stays committed to his mission, providence will manage the rest. Ultimately, there is no contradiction between imagination and practicality. By pursuing his dreams, Ray not only discovers a way to settle his debts—thanks to tourists flocking to the enchanted ballpark—but also ensures his ability to keep living on the farm.

The novel focuses on the bond between a father and his son. Ray's father instilled a passion for baseball in him and deeply admired Shoeless Joe, believing he was unjustly banned from the game. This admiration is why Shoeless Joe is the first player to appear on Ray's baseball field. It provides Joe an opportunity to correct the wrong done to him and lets Ray honor the memory of his father, who passed away twenty years earlier.

When Ray initially meets and talks with Shoeless Joe, his thoughts quickly turn to his father, hoping he could join the resurrected White Sox as a catcher. When this hope becomes reality, and he sees his father as a young man of twenty-five, Ray feels hesitant about how to interact with him. Yet, once he decides to approach his father as a friend, he starts considering all the subjects he wishes to explore: "I'll guide the conversation … and we'll hardly realize that we're talking of love, and family, and life, and beauty, and friendship, and sharing." Kinsella communicates a straightforward message: those we cherish can stay close, even after they pass away, if we keep our hearts and minds open; the gap between the living and the dead isn't as intimidating as it seems.

Ray's twin brother, Richard, immediately benefits from Ray's discovery. Unlike Ray, Richard had a disagreement with their father and didn't reconcile with him before he died. Ray assists the initially confused Richard in seeing their father at the ballpark, enabling Richard to also experience the renewed family unity.