Rapid global changes since the last deglaciation can be well documented in marginal sea sediments, while isolating individual paleoenvironmental signals is still challenging. Here, we identified magnetic minerals and unmixed their variations in sediments from the northwestern South China Sea to decipher environmental variations since the last deglaciation. The variation in the hematite to goethite ratio indicates a relatively drier mid‐Holocene and a wetter early and late Holocene in the Red River catchment. The position shift and intensity variation of Western Pacific Subtropical High may account for the Holocene precipitation changes. A higher chemical weathering intensity accompanied by a relatively more fine‐grained magnetite input during the last deglaciation suggests decoupling of the Asian Summer Monsoon and chemical weathering in the catchment, which might have been caused by the shelf exposure during the deglaciation. In addition, the relative abundance of biogenic magnetite increased with the sea level and possible deep‐water temperature rise. Therefore, magnetic minerals such as hematite, goethite, detrital and biogenic magnetite are markedly potential fingerprints for continent‐ocean environmental changes.