Microplastics are ubiquitously found in the environment; however, our knowledge about their storage and mechanism in the burial record is scarce. We selected a core (CCYY1) in the tidal flat of the Yangtze Estuary and investigated its microplastic pollution and sediment grain size. Both plastic production and sediment grain size were significantly positively correlated with microplastic abundance, revealing that the distribution of microplastics in the core was mutually affected by plastic production and extreme flood events. Moreover, the sedimentary record increased rapidly in microplastic abundance and microplastic diversity during the historic extreme flood. The resuspension of upstream microplastics and erosion of land-based microplastics by heavy rain may be responsible for the increase during flood events. Microplastic abundance had a significant period of 8 a and 22 a, indicating the influence of El Niño-Southern Oscillation and solar activity. This study also proposed microplastics as a proxy index for palaeo-flooding.