Abstract: By analyzing the measured data of hydrology and salinity during the spring tide of the dry season in the Modaomen waterway, the differences of the upper and lower velocity structure near the halocline during flood and ebb are demonstrated, the characteristics of change of salinity and salt water wedge are determined, and the Modaomen estuary is classified as a partially mixed estuary. Three stratification indexes including the overall Richardson number, gradient Richardson number and potential energy are calculated to analyze the periodic stratification-mixing process of vertical water layers with different densities, and the stratification-mixing peak time is pointed out. The Simpson potential energy theory is applied to study the processes of estuarine circulation, tidal straining and tidal stirring in the Modaomen waterway. It is revealed that there are corresponding relationships between the above three processes and the peak values of the stratification indexes. The results imply that during the spring tide of the dry season, estuarine circulation promotes stratification while tidal stirring plays the opposite role. Tidal straining suppresses stratification during flood, and during ebb it induces stratification. The tidal straining is the main control factor of the periodic stratification-mixing process of different density water layers in the Modaomen waterway.