Abstract Magnetic minerals preserved in marginal‐sea sediments can serve as distinct fingerprints for unraveling paleoenvironmental evolution. However, the forcing mechanisms that govern the transport and accumulation of individual magnetic minerals at orbital timescales remain poorly constrained. Hence, we present a systematic environmental magnetic analysis performed to isolate the relative abundances of detrital magnetite and hematite in core CJ04‐59 from the Ninety‐east Ridge. The detrital magnetite varies mainly with precession cycles, while the detrital hematite responds more clearly to obliquity cycles. Detrital magnetite is preferentially formed in water‐logged fluvial floodplains subjected to Indian summer monsoon precipitation variations, whereas detrital hematite is preferentially formed in the arid interior of Asia and subsequently transported by winter monsoon in response to obliquity‐driven meridional insolation contrasts. Therefore, isolation of different magnetic signals can help to better understand the independent mechanism governing these marginal seas in the recent past.