While critically neglected for the better part of the 20th century, interest in Willa Cather was aroused in the 1980s with the rise of the feminist movement. Although many of her novels have been subsequently incorporated into the canon, critics have largely ignored The Professor’s House, passing it over on account of it being “morally and psychologically unachieved”. As a reason for this disparagement, critics often cite the “broken” format of the book, rebuking its structure as unnecessary. Or, they cite the ambivalent depiction of the Professor’s psyche. The reader is unsure of how to consider the Professor’s demands for solitude and his entrapment in the past. He’s a family man and a university man, but the Professor’s conflict reaches its crux when he surrenders "local community for the nostalgic national ideal". A.S. Byatt calls The Professor's House Cather's "masterpiece... almost perfectly constructed, peculiarly moving, and completely original".
The Professor’s House has been criticized as “fragmentary and inconclusive” because of the way the middle section, “Tom Outland’s Story,” fractures the surrounding narrative.
J. Schroeter presents the most common critical view regarding the structural meaning of the novel in his essay “Willa Cather and The Professor’s House”: "Book II is the 'turquoise' and Books I and III are the 'dull silver'. The whole novel, in other words, is constructed like the Indian bracelet. It is not hard to see that Willa Cather wants to draw an ironic contrast not only between two pieces of jewelry but between two civilizations, between two epochs, and between two men, Marcellus [sic] and Outland, who symbolize these differences".
Some critics, however, have analyzed the novel’s structure in light of the sonata—equating the novel with either a complete, three-movement sonata, or a single sonata, broken up into exposition, development and recapitulation. Other critics, such as Sarah Wilson, cite the Dutch painting style, which Cather references in her correspondence, as a way of explaining the novel’s theme and layout. Dutch paintings provide a sense of the context beyond the actual objects presented. They consist of crowded interiors and, in Cather’s words, “a square window, open…The feeling of the sea that one got through those square windows was remarkable, and gave me a sense of the fleets of Dutch ships that ply quietly on all the waters of the globe—to Java, etc.’’ Applied to The Professor’s House, Books I and III serve as the overstuffed Dutch interior, while “Tom Outland’s Story, with its more open setting and voice, functions as the open window.
In recent years a Queer reading of The Professor’s House has emerged. This reading centers on the professor’s relationship with Tom, as well as Tom’s relationship with his idolized friend Roddy. Through Tom’s youthful influence, the professor achieves a sort of procreation—his work comes forth more easily and fluidly. “Tom represents the Professor’s need to live with delight.” For the professor, Tom’s loss also represents the professor’s forgoing of homoerotic desire and along with it, a life “without delight... without joy, without passionate grief”. Tom and Roddy share a deeply intimate experience of discovery. Tom views Roddy’s selling of the find as a betrayal, and they experience a split with characteristics of a romantic rift.