In this study, the Sr isotope ratios (IRs; 87Sr/86Sr) of ferromanganese (Fe–Mn) crusts are analyzed through laser ablation inductively coupled plasma multiple-collector mass spectrometry. A sample collected from off Minamitorishima Island showed uniform Sr IRs (0.70906–0.70927) similar to that of present-day seawater with more than 36 mm thickness. Meanwhile, a detritus-rich sample collected from off northeast (NE) Japan showed a wide variation in Sr IRs (0.707761–0.709963). The Sr IR variation in the Fe–Mn crust from off NE Japan suggests detrital influx contributions from both the NE Japan arc (<0.708) and aeolian dust from China (>0.718). Detrital flux from the NE Japan arc increases from the bottom to middle layers, possibly due to the uplift of the Ou backbone range that occurred after ~2 Ma. The increased influx of the aeolian dust in the outer layer is attributable to global cooling in the Quaternary that increased the loess dust transportation from China to the western North Pacific Ocean. Meanwhile, the influence of the detrital influx on the sample from off Minamitorishima Island appeared to be negligible. The Sr IR analysis with high spatial resolution proposed in this study possibly improves the burial history of Fe–Mn nodules.