Based on the historical flood disaster data from 1950 to 2018, the spatiotemporal distribution of agricultural disasters caused by floods and waterlogging in China was studied by two selected indexes, the agricultural disaster area and disaster affected area, combined with the nine point quadratic smoothing, time series analysis and spatial clustering methods. The results show that on the time scale, the impact of floods and waterlogging on agriculture in China has an overall increasing trend from 1950 to 2018, but there are obvious differences in different regions. Flood and waterlogging disasters have a great impact on agricultural development, and this situation may continue in the next few years. On the spatial scale, the agricultural disaster in South China, some parts of Northeast China and coastal cities is more serious than that in other regions.