Objectives: To evaluate the operative performance and efficiency of clinical sections and its improvement year by year using Data Envelopment Analysis (DEA) Methods: We evaluated the operative performance of each clinical section in a regional teaching hospital using the DEA method. The Decision Making Units (DMU) includes 7 sections of the internal medicine group, and 12 sections of the surgical group. The study was conducted using data in years 2004 to 2005. The two input variables were the number of attending doctors and nurses, and the three output variables were OPD and emergency case number, admission day medical income. The aforementioned data was analyzed with the CCR model of the DEA method to obtain the relative efficiency scores of various sections in the hospital, after which a comparison was made between the relative efficiency score of sections in the internal medicine group and those belonging to the surgical group. Finally, we discuss the shift in technology and catching up in efficiency by calculating cross-year efficiency score according to the Malmquist index. Results: The average efficiency score of the internal medicine group in the cross-year was 96.25%, and the average efficiency score of the surgical group in the cross-year was 84.03%. This result indicates that the operative performance of the internal medicine group in this hospital is higher than that of the surgical group. The average efficiency score of all the clinical sections in the year 2005 was 92.29%, which also indicates a higher operative performance than the 87.28% in 2004. From calculations according to the Malmquist index, we can see that there are 14 sections whose performance is increasing year by year. Conclusions: By using the CCR model of DEA, we can distinguish the performance of each clinical section; by suing the Malmquist index, we can follow trend of improvement or recession year. There results can help the decision-maker of the hospital use resources allocation correctly to achieve the optimal level of the institution.