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Using a recently developed functional analysis tool, Multiscale Window Transform (MWT) and the MWT-based theory of canonical transfer, this study investigates the dynamical processes responsible for the seasonal variability of the mesoscale eddies in the South China Sea (SCS). A three-scale energetics framework is employed, in which the original fields are decomposed into subfields on a nonstationary background flow window, a mesoscale eddy window and a high-frequency synoptic eddy window. Three local regions of high mesoscale eddy kinetic energy (EKE) levels, namely, the southwest of Taiwan Island (SWT), the southeast of Vietnam (SEV) and the northeast of the Natuna Island (NEN), are identified. The seasonal cycles of the mesoscale EKE in the three regions are not in phase, with peaks occurring around January, October and December, respectively. By diagnosing the canonical transfers between the background flow and the mesoscale eddies, we find that the seasonal cycle of the eddy variability in the SWT region is due to a mixed instability (baroclinic and barotropic instabilities), while barotropic instability plays a dominant role in determining the EKE seasonality in the SEV and NEN regions. This is quite different from the previous argument that baroclinic instability dominates the seasonal EKE in the SCS. The three-scale framework further reveals that high-frequency synoptic motions act to dissipate the lower-frequency mesoscale eddies through forward energy cascades. Besides the internal processes, external wind forcing is also found to influence the seasonal eddy variability, but is only limited to the NEN region. Our results highlight different mechanisms controlling the seasonal modulations of the mesoscale eddies in different regions of the SCS. • A Mixed instability controls seasonal eddy variability southwest of Taiwan. • Barotropic instability dominantly controls the eddy energy seasonality. • Wind only influences the seasonal eddy variability northeast of the Natuna Island. [ABSTRACT FROM AUTHOR]