In order to study the effects of waterlogging and drought alternative patterns on fluorescence parameters and photosynthetic characteristics of rice at different growth stages under controlled irrigation and drainage condition, pit rice planting experiments were performed by taking farmland water level as the control index. Two alternative patterns of waterlogging and drought were set up: waterlogging after drought (HZL) and drought after waterlogging (LZH) in the tillering stage, the jointing and booting stage, the heading and flowering stage and the milky maturity stage. And the relative chlorophyll content (SPAD), fluorescence parameters and photosynthetic indicators were observed. The results showed that alternate waterlogging and drought stress reduced SPAD, and HZL treatment produced stronger inhibition. Fluorescence parameters and photosynthetic indicators of alternate waterlogging and drought stress, including the light energy conversion efficiency, photosynthetic quenching coefficient, maximum potential electron transfer rate, light saturation point, net photosynthetic rate, optional water use efficiency in the tillering stage and the jointing and booting stage can restore or even exceed the control level, in the flowering stage and milk stage had irreversible effects. Transpiration rate and stomatal conductance were inhibited respectively in the tillering stage and the milky stage, and promoted in the jointing stage. HZL treatment improved nonphotochemical quenching coefficient, and other major fluorescence parameters and photosynthetic index of HZL were lower than LZH treatment. LZH treatment in the tillering stage and jointing stage was more effective in compensating for photosynthesis. The inhibition of photosynthesis of HZL treatment in the heading and flowering stage was more obvious than that of LZH treatment. Therefore, alternate waterlogging and drought stress should be avoided in the late growth stage of rice, especially drought turned to waterlogging sharply.