The purpose of this study was to establish a mangerial evaluation system for scientific research based on entropy-weighted TOPSIS approach that includes evaluation descriptors to comprehensively evaluate the scientific research capability in hospitals. The study showed that the first three evaluation descriptors with highest weights were the number of patent grants (0.2368) , total money (0.1141) and number (0.0925) of technology transfer contracts. Among the 13 hospitals included in this study (A1~A13) , A12 boosted the strongest capability while A4 appeared weakest in scientific research. A huge difference was apparent in similarity scores between the strongest and the weakest (by nearly 27-fold) . This study objectively quantified the critical factors that led to the difference in capabilities of scientific research in hospitals, and would help guide sustained improvement of the scientific research capabilities in these hospitals. Meanwhile, this study also provide methodological evidence for health administration authority in policy-making.