Pecan cuttings are difficult for rooting. This study describes the pecan hardwood rooting process based on anatomic characteristics to understand root formation mechanisms of pecan cuttings. The expressed proteins of different periods during the adventitious rooting process of pecan seedling hardwood cuttings were identified and analyzed to evaluate the rooting mechanism. The expressed proteins of pecan cutting seedlings were also compared with other cultivar cuttings during the rooting period. Pecan seedling cuttings were developed at different air and substrate temperatures to induce root formation. Adventitious root formation of pecan hardwood cuttings was described, and the phloem at the base of the prepared cuttings was selected as the sample for the differential protein analysis. The results showed that adventitious root formation of pecan hardwood cuttings was the only product of callus differentiation, which originated from the cells of the cambium or vascular ray parenchyma. Such adventitious root primordia were developed from those calluses that formed the regenerative structure, and the expressed proteins during the adventitious rooting of pecan hardwood cutting were identified and analyzed by matrix-assisted laser desorption ionization–time of flight–mass spectrometry (MALDI-TOF-MS) to evaluate the rooting mechanism. Eight differentially expressed proteins were found in the rooting periods, and 15 differential proteins were found by comparing pecan cutting types, which were analyzed by peptide mass fingerprinting homology. The results show that the primordial cells were differentiated from the meristematic cells. Furthermore, the differentially expressed proteins contained energy metabolism proteins, adversity stress proteins, and signal transmission proteins. The energy metabolism-related proteins were adenosine triphosphate (ATP) synthase, photosynthesis-related proteins, and enolase. The adversity-stress proteins containing heat shock-related proteins and signal transmission proteins were mainly cytochrome enzymes and heme-binding proteins. Adventitious root formation of pecan cultivar hardwood cuttings was difficult. More trials should be performed from the potential aspects of high defensive protection and phloem morphologic structure.