The aquatic eco-environment is significantly affected by temporal and spatial variation of the mixed layer depth (MLD) in large shallow lakes. In the present study, we simulated the three-dimensional water temperature of Taihu Lake with an unstructured grid with a finite-volume coastal ocean model (FVCOM) using wind speed, wind direction, short-wave radiation and other meteorological data measured during 13-18 August 2008. The simulated results were consistent with the measurements. The temporal and spatial distribution of the MLD and the possible relevant mechanisms were analyzed on the basis of the water temperature profile data of Taihu Lake. The results indicated that diurnal stratification might be established through the combined effect of the hydrodynamic conditions induced by wind and the heat exchange between air and water. Compared with the net heat flux, the changes of the MLD were delayed approximately two hours. Furthermore, there were significant spatial differences of the MLD in Taihu Lake due to the combined impact of thermal and hydrodynamic forces. Briefly, diurnal stratification formed relatively easily in Gonghu Bay, Zhushan Bay, Xukou Bay and East Taihu Bay, and the surface mixed layer was thin. The center of the lake region had the deepest surface mixed layer due to the strong mixing process. In addition, Meiliang Bay showed a medium depth of the surface mixed layer. Our analysis indicated that the spatial difference in the hydrodynamic action was probably the major cause for the spatial variation of the MLD in Taihu Lake.