The theme of nature is deeply linked to happiness, longevity, and vitality in the poem. The poet explains that people live in cities and slowly die every day because they're separated from nature. He also believes that nature—unlike humanity—is eternal. Life can be found in that vitality, and not in the city where a person tries to live out his or her daily routine. The speaker compares the city itself to nature, saying that it's the "high reef of the human dawn" and the "mother of stone."

Neruda also explores the nature of humanity. The speaker tries to find the spirits of the people who lived in Macchu Picchu. He asks them to reveal themselves to him. He wonders whether the people who built the city were slaves. He speculates on how people live their lives in cities and how it disconnects them from happiness and health. He says that humans are only mortal and are unable to last forever—unlike nature.

Resurrection is another theme in "The Heights of Macchu Picchu." By the end of the poem, the poet has connected with the people who built Macchu Picchu and wants them to be reborn along with him. He wants to find his immortality in the structures of Macchu Picchu that remain standing long after the people are gone—and he wants them to experience that too. He tells them to "fasten your bodies to me like magnets" and to "speak through my words and my blood."