Abstract: As the estuary with the richest biodiversity in China, the marine environment of the Yangtze River Estuary is very important to study the effects on distribution and abundance of aquatic living resources. However, in the current comprehensive monitoring survey of the Yangtze River Estuary, there is a lack of optimization process in the design of monitoring stations. In order to evaluate the impact of different sampling designs on the monitoring results of marine environment in the Yangtze River Estuary, the ordinary Kriging (OK) was used to interpolate the spatial distribution of different marine environmental factors. And sampling effects of stationary sampling (SS) , simple random sampling (SRS) and stratified random sampling (StRS) on water temperature, salinity, dissolved oxygen and chemical oxygen demand (COD) of the Yangtze River Estuary were compared. The results show that: 1) the environmental factors of interpolation results were similar to survey value, OK can better simulate the study area of the "true" Marine environmental conditions; 2) the average design effect (DE) of the three sampling designs was as follows: StRS>SS>SRS; 3) the sampling effect of the three sampling designs for COD has little difference, and the StRS is the best among the water temperature, DO and salinity. Salinity has obvious spatial distribution characteristics in the Yangtze River Estuary. In order to meet the monitoring needs of most factors, it is recommended to using StRS in the future comprehensive investigation and monitoring.