Objective To evaluate the implementation effects and problems about quota payment of specific diseases for hyperplasia prostate and ureteral calculi in Chengdu. Methods Payments, man-time of operation, and the lengths of hospitalization of hyperplasia prostate and ureteral calculi as quota payment of specific diseases in Chengdu from 2013 to 2015 were analyzed by using SPSS 16.0 software. Results Based on the standards of medical expense limitation in Chengdu unchanged, tertiary and secondary hospitals remained surplus with quota standards of single diseases unchanged. The average lengths of hospitalization of hyperplasia prostate and ureteral calculi in tertiary and secondary hospitals were significantly decreased (P<0.05). Conclusion The application of quota payment policy for single disease in Chengdu city of Sichuan province has been proved to work on controlling the medical expense of treating hyperplasia prostate and ureteral calculi. Our results indicate the continuous implementation of quota payment policy. However, the exploration of proper payment standardization, enhance of hospital supervision and establishment of efficient system are still needed to define.