The seasonal variation of intermediate meridional overturning circulation (IMOC) in the South China Sea (SCS) is investigated using the Simple Ocean Data Assimilation version 2.2.4 (SODA2.2.4) product for the period of 1950–2010. The SCS IMOC displays distinct seasonal features, with a counterclockwise cell dominating the interior SCS (12∼18°N, 200∼700 m) in winter and a broader clockwise cell occupying the region for (7∼20°N, 50∼900 m) in summer. By removing the 12-month average, the main characteristics of the seasonal IMOC is captured deeply. There is a counterclockwise anomaly in winter and a clockwise anomaly in summer occurring in the region for (8∼20°N, 100∼1000 m). And the strongest anomalies of the overturning stream functions are mainly located in (12∼17°N, 200∼400 m) that is taken as the representative region to study the seasonal IMOC. A dynamical decomposition of the IMOC seasonal anomaly allows a further look into the seasonal variation of the SCS IMOC. The IMOC seasonal anomaly is decomposed into three components: the Ekman component, the vertical shear component, and the external component. The Ekman component exhibits a full cell clockwise in winter and counterclockwise in summer with a negative contribution to the IMOC anomaly. The vertical shear component has a strong cell counterclockwise in winter and clockwise in summer occupying most of the areas above 1000 m with a positive contribution to the IMOC anomaly. The external component has a relatively complex structure, and its positive and negative contributions to the IMOC anomaly alternate with increasing latitude at 200∼1000 m. According to the seasonal fractional covariance of these three components on the IMOC anomaly in the representative region, the vertical shear component and the Ekman component have the main contributions to the IMOC seasonal anomaly, and the external component has a limited impact. The vertical shear and its meridional difference can lead to a downward motion at around 12°N and an upward motion at around 17°N in winter, and reverse motions in summer. The seasonal vertical motions will cause an overturning counterclockwise in winter and clockwise in summer. The Ekman component is mainly driven by the monsoon over the SCS that generates the Ekman transport northward in winter and southward in summer. The seasonal Ekman transport and its return flow together form an overturning clockwise in winter and counterclockwise in summer. And the external component counterclockwise in winter and clockwise in summer between 14°N and 17°N is associated with the horizontal flow northeastward in winter and southwestward in summer zonally going over shallower or greater depths, which can induce seasonal reverse upwelling and downwelling at different latitudes.