Warm-sector heavy rainfall (WSHR) frequently occurs in South China, causing severe floods and posing serious threats to human health and societal systems there. However, its moisture sources, transport pathways, and triggering mechanisms still warrant in-depth investigations. Here we identify three different clusters of moisture sources and transport pathways of WSHR in South China during 1982–2015 and reveal their associated atmospheric circulations and local-scale convection patterns. In the case of cluster 1, a strong anomalous high-pressure system and an anomalous low-pressure system jointly induce strong southwesterly air-flows, and a local convergent flow and ascending motions appear over the west of South China, thereby providing sufficient water vapor from the Indian Ocean and favorable dynamical conditions for triggering WSHR events in the west of South China. In contrast, the trajectories of cluster 2 are characterized by strong easterly air-flows that supply a large amount of water vapor from the Northwest Pacific and induce a strong convection, favoring the WSHR occurrences in the eastern coastal area of South China. In the case of cluster 3, a high-pressure anomaly and a shallow low-pressure system respectively cover the southeast and northwest portions of South China. This circulation pattern causes a strong anomalous southerly wind and induces an anomalous convergent flow over entire South China, thereby transporting sufficient water vapor from the South China Sea and triggering WSHR events over South China. Differing from WSHR, the moisture of frontal heavy rainfall events over South China is not only contributed by the three dominant ocean-originating moisture transport paths but also by the continent-originating paths. The findings reported here highlight that the atmospheric trajectories and synoptic systems jointly modulate the spatial variation of heavy rainfall events in South China by dominating large-scale transport pathways of water vapor and local-scale convection patterns.