Frequent flood disaster causes great loss of rice planting. Therefore, the study on the influence of frequent flood disaster on the agricultural productivity of rice planting and the structural optimization strategy was put forward. Firstly, the data of experimental area were used to design the implementation period, duration of flooding, flooding depth, experimental plot and contrast plot, and then appropriate analysis methods were selected to test the influence of frequent flood disaster on agricultural productivity of rice planting. Experimental results show that if the waterlogging time is more than three days, the production efficiency will decrease by more than 50%. The earlier the flood happens, the more serious the influence on production efficiency. Based on the experimental results, the optimization strategies of rice planting agricultural structure are formulated as follows: reasonable layout, overall improvement of land economic efficiency and utilization; optimization of rice varieties and improvement of rice quality; deepening of farmers' organizational degree, improving the agricultural scale of rice planting; promoting the development of rural science and education, adjusting the industrial structure of rice planting agriculture, and perfecting the rice planting industry chain.