In the tributary backwater area, the Three Gorges Reservoir, impoundment after flooding season often results in phosphorus accumulation. Meanwhile, algal blooms occur almost every year in late winter. To find their relationship, we studied the activity of alkaline phosphatase(alkaline phosphatase activity of phytoplankton-PAPA and total alkaline phosphatase activity-TAPA) and different phosphorus forms during January and March 2013. Results showed that TAPA, maximum reaction rate for total alkaline phosphatase V_max, PAPA/TAPA and PAPA/Chl.a flunctuated greatly, reaching the first and second peak at the middle of February and March respectively. According to the characteristics of the algal blooms, we divided it into four periods Ⅰ, Ⅱ, Ⅲ and Ⅳ. The first is induction period, during which SPR was mainly from the decomposition of organic phosphorus by alkaline phosphatase of phytoplankton and meanwhile, algae presented excessive intake of phosphate. The second is transition period, when water temperature and alkaline phosphatase activity was relatively low. The third is bloom stage, during which the alkaline phosphatase was mainly from the germs, chlorophyll-a concentration reached the maximum and SPR the minimum. The last is the ending period of the algal bloom, the alkaline phosphatase was also mainly from the germs, chlorophyll-a concentration decreased and soluble reactive phosphorus concentration increased gradually.