The Yellow Sea Warm Current (YSWC) and Yellow Sea Cold Water Mass (YSCWM) are crucial components of Yellow Sea oceanic dynamics. Investigating their historical relationships since the mid-Holocene, as demonstrated by modern observations, is highly important. We reconstructed their evolution using 37 surface sediment samples and core Z1 from the Yellow Sea. Basic end-member analysis of core sediment grain sizes revealed that end-member two had a dominant peak at 12 μm, indicating the evolution of the YSWC. The analysis of the structure of benthic foraminiferal communities in surface sediments indicated that the combination of Ammonia ketienziensis, Hanzawaia nipponica, and Astrononion italicum serves as a reliable indicator of the evolution of the YSCWM. By integrating sedimentological and micro-palaeontological evidence with published organic geochemical findings, we elucidated high-resolution evolutionary records of the YSWC and YSCWM since the mid-Holocene. Our findings indicate that the YSWC underwent rapid intensification with significant fluctuations during ∼6.0–3.9 ka. It then decreased to modern levels between ∼3.9 ka and ∼1.9 ka, remaining relatively stable during ∼1.9–0.0 ka, with enhancements noted at ∼1.4 ka and ∼0.3 ka. The YSCWM evolved synchronously with the YSWC after ∼6.0 ka, weakened and then strengthened during ∼6.0–1.9 ka, and maintained relative stability during ∼1.9–0.0 ka, with decreases observed at ∼1.4 ka and ∼0.3 ka. The YSWC and YSCWM exhibited opposite changes, similar to modern oceanographic patterns, except for synchronous variations during ∼4.0–3.9 ka, when the YSCWM was formally established. The decoupling of the YSCWM and the YSWC during ∼4.0–3.9 ka and the significant enhancements of the YSCWM at ∼2.5 ka and ∼2.0 ka when the YSWC slightly weakened are associated with the substantial influence of the ENSO climate phenomena on the coastal regions of East Asia from ∼4.0 ka to ∼1.9 ka. We propose that the YSCWM is more sensitive to ENSO, potentially making it more suitable for reconstructing the palaeoceanography and palaeoclimatology of the Yellow Sea.