In order to study the effects of the compound microbial organic fertilizer on photosynthetic characteristics and yield of rice under watersaving irrigation conditions in cold region and black glebe, experiment with four compound microbial organic fertilizer application levels, which were 20kg/hm2(OF20),40kg/hm2(OF40), 60kg/hm2 (OF60) and 80kg/hm2(OF80) were carried out under the water-saving irrigation regime, meanwhile the inorganic fertilizer was taken as control treatment (CK). The photosynthetic characteristics and yield were studied. The results demonstrated that the net photosynthetic rate (Pn), the maximum photochemical quantum efficiency (Fv/Fm), the reaction center potential activity (Fv/Fo) and the excitation energy capture efficiency (F′v/F′m) were increased firstly and then decreased with the increase of compound microbial organ fertilizer at each stage, so did the actual photochemical quantum efficiency (ΦPSⅡ) and photochemical fluorescence quenching coefficient (qP) at heading and milky stage, and approaching the best values in OF60 plot. However, the stomatal limit value (Ls) was decreased firstly and then increased with the increase of compound microbial organic fertilizer, which was less than CK. Across all treatments, for the nonphotochemical quenching coefficient (qN), no significant difference was found at 5% level. Among the different treatments, the highest yield was obtained in OF60 plot as well as the rice quality was better. Therefore, under OF60 regime was the best. It could provide a theoretical basis and reference for the application compound microbial organic fertilizer under watersaving irrigation conditions in cold region and black glebe.