Abstract The South China (SC) late rainy season rainfall (SCLR) is important to people’s livelihoods and properties of this densely populated and economically developed region. Based on observation and reanalysis datasets, this study identifies that the relationship between the SCLR and equatorial Pacific SSTs (EPSSTs) experiences an interdecadal change around the late 1970s. The SCLR is negatively correlated with the eastern EPSSTs during 1948–1977 (the previous epoch) but positively correlated with the central EPSSTs during 1978–2022, especially during the last three decades 1993–2022 (the post epoch). This is due to the interdecadal change in El Niño flavors and EPSSTs-tropical Atlantic SSTs (TASSTs) relationship. With the increasing frequency of central Pacific El Niños in the post epoch, the El Niño-related warm SST anomaly center shifts from the eastern equatorial Pacific (EEP) to the central equatorial Pacific (CEP). Correspondingly, the anomalous cyclone exerted by the CEP warming reaches SC and causes rainfall surplus there (westward propagation pathway). In contrast, the EEP warming in the previous epoch can’t influence the SCLR through the westward propagation pathway, but through shifting the westerly jet southward via heating the tropical troposphere. The southward shifted westerly jet crashes the Qinghai-Tibet Plateau, triggering cyclonic circulations across the northern East Asia and North Pacific, which in turn cause anticyclonic circulations over the western SC and reduce SC rainfall (eastward propagation pathway). On the other hand, the CEP warming in the post epoch barely influence the SCLR through the eastward propagation pathway because of the enhanced negative relationship between EPSSTs and TASSTs.