Objective To retrospectively analyze the CT findings of less than and equal to 3cm papillary renal cell carcinoma and clear cell renal cell carcinoma in order to improve the level of their differential diagnosis. Materials and Methods Retrospective analysis of the CT scanning images of 11 cases PRCC and 44 cases CCRCC being confirmed by pathology, including kinds of CT signs, density values and the degree values of enhancement of various times of the lesions. And the statistical analysis of the corresponding materials were carried on. Results The CT characteristic differences of necrosis or cystic degeneration within the tumor, unenhanced boundary, and enhanced uniformity of PRCC and CCRCC have statistics significance (p < 0.05). The differences of the tumor diameter, the shape, the calcification, the hemorrhage within tumors, position of lesions centrality, unenhanced density and enhanced way of two groups of cases have not statistics significance (p>0.05). The density value and enhanced degree of the tumors in cortex medulla period and early drainage period in both of the two cases have obvious difference. The two period of enhanced density values and enhanced degree values of PRCC are lower than CCRCC. Conclusion Necrosis or cystic degeneration within tumor, tumor unenhanced boundary, tumor enhanced uniformity, tumor enhanced density value and enhanced degree value play an important role in the two differential diagnosis.