A multi-factor and multi-objective optimization method based on orthogonal experiment and entropy weight method is proposed to investigate the influence of the parameters such as rotational angular speed (omega), operating temperature (T), relative humidity (RH), and operating pressure (P) on the performance indicators of rotary proton exchange membrane fuel cell (R-PEMFC), and to comprehensively evaluate the performance of R-PEMFC through multiple objectives. The results show that different parameters have various degrees of influence on different performance indicators. Moreover, the weights of each performance indicator are determined by the entropy weight method, in which the effective mass transfer coefficient accounts for the largest weight of 24.11 %, followed by the oxygen uniformity index, net power density, temperature difference and current density uniformity index accounting for 18.99 %, 16.10 %, 15.66 %, and 15.47 %, respectively, and the pressure drop accounts for the smallest weight of only 9.67 %. Finally, according to the weight, the orthogonal experimental schemes are comprehensively scored, and it is known that the best omega is 1080 rpm, T is 353 K, RH is 50 %, and P is 1.6 atm. This investigation has supplied a multi-objective optimum method and evaluate idea, which has reference value for further improving the performance of R-PEMFC.