By analyzing the measured data of hydrology and salinity in the North Passage of the Yangtze River Estuary in 2016, it is found that the salt water wedge exist and the salinity stratification is stronger during neap tide than spring tide. The Simpson potential energy was applied to study the temporal and spatial variation of the mixing and stratification of the North Passage, and the extreme value of potential energy anomalyat the upper and middle of North Passage appears at the high slack and low slack while it appears at the max flood and max ebb at the lower part of North Passage. The improved one-dimensional potential energy difference equation was used to analyze the spatial and temporal changes and corresponding relationships of tidal strain, estuarine circulation, river effect, and tidal stirring during the dry season in the North Passage. It is found that the trend of mixing and stratification of the water body is determined by the relative sizes of these four factors, and the mechanisms that affect the stratification changes during the spring and neap tide are tide stirring, estuarine circulation and river effect. It is found that the estuarine circulation is the main dynamic mechanism for promoting estuary stratification during flood tide; the river effect is large during the ebb, and the average tide effect is stronger than the tidal strain, which promotes the estuary stratification as a whole; the tide stirring in the spring tide is 1 to 2 orders of magnitude larger than the neap tide, which weaken the stratification. And the improved one-dimensional potential energy difference equation can better explain the mixing and stratification characteristics of Yangtze River Estuary.