Global mean sea level (GMSL) during intermediate interglacial Marine Isotope Stage 3 (MIS 3) (60–26 ka) has proven difficult to constrain. Paleo‐sea level estimates based on ice margin, modeling, and paleo‐shoreline reconstructions indicate that MIS 3 GMSL was substantially higher than reconstructed from deep‐ocean benthic foraminifera oxygen isotope (δ18O) and coral records, implying much smaller ice sheets during MIS 3. Here, we use the δ18O and Mg/Ca chemistry of surface and thermocline dwelling foraminifera in the Sulu Sea in the western Pacific margin to estimate relative changes of the influx of South China Sea surface flow through the Sulu Sea over the last 140 ka. We show that this South China Sea throughflow is controlled in part by changes in GMSL modulating the depth of the 36 m deep Karimata Strait at the southern end of the South China Sea. We constrain maximum allowable GMSL at the beginning and end of MIS 3 to −22 ± 6 and −29 ± 5 m, respectively, and minimum allowable GMSL during interglacial stages MIS 5c and 5a (117–72 ka) to range from −3 ± 8 to −8 ± 8 m and −11 ± 7 to −12 ± 7 m, respectively. Our results constrain MIS 3 GMSL, but do not rule out higher MIS 3 ice margin, modeling, and paleo‐shoreline‐based MIS 3 GMSL estimates or lower coral and seawater δ18O‐based estimates. Our results favor the highest MIS 5a and 5c GMSL estimates and confirm that the Sunda Shelf served as a land‐bridge for human and megafauna migration during MIS 3 when humans first arrived in Borneo.