This work concentrates on the processes of stratification and turbulent mixing in a choked shallow lagoon, Xiaohai Lagoon, by using a three-dimensional hydrodynamic model. The model results were processed to derive buoyancy frequency, shear production, gradient Richardson number, and buoyancy flux during the tidal cycles. The parameters regarding stratification and turbulent mixing exhibited significant heterogeneity within the lagoon. Shear production primarily occurred in the downstream region with complex shoreline and bed morphology, whereas stratification was predominantly developed in the flat upstream region by tidal strain and baroclinic strain, especially during the ebb tide. The salinity mixing indicated by buoyancy flux was thus mainly confined during the ebbs in the downstream region and the middle-lower layer of the upstream region. In addition, the distribution of the gradient Richardson number indicated dominances of shear instability and buoyancy effects in the downstream and upstream regions, respectively. By simulating various combinations of river discharges and offshore tidal ranges, we examined the variations of stratification and turbulent mixing within the lagoon's parameter space. The results revealed the influence of the interaction between tidal and runoff forces through a modulation of the salinity interface's moving range. Further investigation of the buoyancy balance underlying the variation in stratification revealed the dominance of straining and mixing, while advection played a secondary role. Straining dominance appeared at locations with sufficient streamwise density gradients in the upstream region during the ebb. The contribution of advection was essential, as straining and mixing largely counteracted each other's effects through their persistent competition. A conceptual model for the stratification and mixing patterns in choked lagoons during the tidal cycle was then proposed. This conceptual model clarifies the process of the interaction between stratification and turbulent mixing in the distinctive hydrological and geomorphic environments of choked lagoons and could serve as a conference for investigating other lagoon systems in the world.