Subsurface chlorophyll maximum (SCM) layers contribute considerably to the integrated biomass of the water column and can be strongly modulated by mesoscale eddies, which are ubiquitous. We examined the influence of mesoscale eddies on the depth, thickness and magnitude of SCM layers in the South China Sea using output from a high-resolution eddy-resolving biological–physical coupled model over a 22-year period. We found that anticyclonic (cyclonic) eddies are responsible for increased (decreased) SCM depth and decreased (increased) SCM magnitude; SCM thickness decreased in cyclonic eddies but slightly increased in anticyclonic eddies. The effects of mesoscale eddies are strongly dependent on eddy amplitude. Maximum anomalies in depth, thickness and magnitude always occur near the center of eddies. Phytoplankton community structures in SCM layers are also affected by eddies, with more diatoms in cyclonic eddies and more coccolithophores in anticyclonic eddies. The results from this study are useful in advancing our understanding of mesoscale physical–biogeochemical interactions.