At first, based on the analysis of factors influencing the efficiency of hospital scientific research activities, the paper sets up the evaluation index system for hospital scientific research activities from aspects of inputs and outputs. Then, by the Principal Component Analysis (PCA), it reduces the dimensionality of the output indexes and conducts efficiency evaluation by Stochastic Frontier Analysis(SFA). At last, it verifies the accuracy and validity of the efficiency model for hospital scientific research activities through practical cases.