Because McPherson draws from such a massive amount of scholarship,Battle Cry of Freedom is not explicitly thesis-driven in the way that a historical monograph would be. Because McPherson deals with so many types of history—military, social, political, and so on—that are often treated separately in other works, it is even more difficult to point to a central argument.

However, one major theme in the work is revealed in the introduction, and that is that both sides in the Civil War spoke about fighting for "freedom." Confederate leaders spoke of defending the "political rights, the freedom, equality, and State sovereignty" that they understood as essential to being American. Of course, McPherson makes it clear that they were also specifically and explicitly fighting to defend slavery, which they linked with each of these abstract concepts, and Union leaders could equally claim to be fighting for freedom. By 1863, they were claiming, through Abraham Lincoln, that a Northern victory would be a "new birth of freedom."

As McPherson observes, the war really was a clash between two visions of liberty, one—the Confederate—unchanged from the past. McPherson says that the "South's concept of republicanism had not changed in three-quarters of a century; the North's had." This was an agrarian vision, one which defined the whole point of government as protecting the property—including human property—of white men. The North, meanwhile, had changed, and its conceptions of freedom had changed with it. Southerners, according to McPherson, feared the "competitive, egalitarian, free-labor capitalism" that the Republican Party represented, and they left the Union to avert the threat this ideology allegedly posed to slavery. At the time, McPherson argues, the North was truly revolutionary, while the South was reactionary. But a central thesis of this book is that all the sacrifice, struggle, and bloodshed resulted in the vision of the North becoming that of the nation. In the future, that vision would continue to be rejected by the South.

James M. McPherson attempts to synthesize the aspects of military and political history and that of social history to provide a comprehensive, synthesized view of one of the most complex periods of modern history, that of the American Civil War period. Of this period, McPherson says that that generation lived "a lifetime in a year." When the history of so short a time is so complex and when synthesis of all historical points of view are attempted in a single volume, then thesis gives way, in the main, to the synthesized points of view.

The editor of McPherson's Oxford HistorySeries published history singles out McPherson's statement that the Civil War generation "lived through an experience in which time and consciousness took on new dimensions" as having thematic importance. McPherson states in his first chapter that cotton from the Southern plantations was, metaphorically speaking, the oil that drove the machinery of England's and New England's industrialization and, thus, economic power, and that, similarly, slavery was the oil that drove the machinery making the South rich and all-important.  

The cascade of cotton from the American South dominated the world market, paced the industrial revolution in England and New England, and fastened the shackles of slavery more securely than ever on Afro-Americans. (Battle Cry of Freedom)

Time and consciousness, as McPherson expressed it, were wrapped up in the ideas of a divided human race (slave and free), an economically dominant form of agriculture and lifestyle, and a privileged position in Western economy. New dimensions of time and consciousness were demanded once the officers who fought together successfully in the Mexican War were called upon to fight against each other in the Civil War, a war that debated (1) the divisiveness of slavery, (2) the privilege of Southern power in Western economy (then, tantamount to world economy), (3) and the unity of their national bonds, the continuance of the United States, as the Civil War was "testing whether that nation, ... [might] long endure" (Abraham Lincoln, "Gettysburg Address"). Based on these concepts, the thesis of Battle Cry of Freedom might be stated as the editor suggests in the Editor's Introduction: The changing meanings of slavery and freedom arose from an experience "in which time and consciousness took on new dimensions," in which was demanded a changing consciousness of the meaning and dimensions of freedom, slavery, and domination.