Temperature extremes not only directly affect the marine environment and ecosystems but also indirectly influence hydrodynamics and marine life. In this study, the role of heat wave events in the occurrence and persistence of thermal stratification was analysed by simulating the water temperature of the North Sea from 2011 to 2018 using a fully coupled hydrodynamic and wave model within the framework of the Geesthacht Coupled cOAstal model SysTem (GCOAST). The model results were assessed against reprocessed satellite data and in situ observations from field campaigns and fixed Marine Environmental Monitoring Network (MARNET) stations. To quantify the degree of stratification, the potential energy anomaly throughout the water column was calculated. The air temperatures and potential energy anomalies in the North Sea (excluding the Norwegian Trench and the area south of 54∘ N) were linearly correlated. Different from the northern North Sea, where the water column is stratified in the warm season each year, the southern North Sea is seasonally stratified in years when a heat wave occurs. The influences of heat waves on the occurrence of summer stratification in the southern North Sea are mainly in the form of two aspects, i.e. a rapid rise in sea surface temperature at the early stage of the heat wave period and a higher water temperature during summer than the multiyear mean. Another factor that enhances the thermal stratification in summer is the memory of the water column to cold spells earlier in the year. Differences between the seasonally stratified northern North Sea and the heat wave-induced stratified southern North Sea were ultimately attributed to changes in water depth.