As a semi-permanent circulation system at the upper troposphere, the South Asian high (SAH) profoundly influences the Asian climate. However, its impact on the underlying tropical cyclone (TC) genesis in the South China Sea (SCS) remains unknown. Here we show that the leading mode of eastern-central SAH and TC genesis (TCG) number in the SCS during July–September are significantly correlated with a correlation coefficient of − 0.71 during 1979–2017. During the strong SAH years, the SAH-related upper-level convergence favors descending motion and low-level divergence in the SCS, decreasing mid-level humidity and low-level vorticity and thus suppressing TCG in the SCS. We find that the variations in the leading mode of eastern-central SAH are coupled to the meridional gradient in surface temperature over the western North Pacific. An enhanced meridional surface temperature gradient can increase the meridional gradient in 200 hPa geopotential height and thus intensify the SAH. Meanwhile, the intensified SAH and the related descending motion, in turn, re-enforce the meridional surface temperature gradient through positive SST-cloud-shortwave radiation feedback. The positive feedback between the SAH and the WNP meridional temperature gradients provides persisting large-scale circulation anomalies that influence the TCG in the SCS from July through September. These results highlight the importance of the SAH and its interaction with the WNP meridional temperature gradients for regulating the SCS TCG and suggest that the precursors that are known to be linked to the SAH intensity can be used to the seasonal prediction of TCG in the SCS.