During the summer of 2016, the northern East China Sea and the southern Yellow Sea (NECS‐SYS) experienced one of the most severe and devastating marine heatwaves (MHWs) on record, with a temperature anomaly exceeding 4°C. This shallow semi‐enclosed continental shelf region is widely recognized as a significant hotspot for MHWs with associated incidences of harmful algae blooms. Previous studies have highlighted the importance of mixed layer shoaling as a crucial factor in the genesis of MHWs in the global ocean. The current study employed the Hybrid Coordinate Ocean Model reanalysis data set during 1994–2015 to delve into the mechanisms driving mixed layer shoaling during NECS‐SYS MHW genesis. Our findings reveal the significant role of the northward propagating boreal summer intraseasonal oscillation in promoting MHW genesis and intensification. Specifically, boreal summer intraseasonal oscillation phases 5, 6, and 7 contribute to the favorable conditions that facilitate MHW formation by inducing mixed layer shoaling and increasing solar influx, with mixed layer shoaling playing a more dominant role. The current study provides insights into the relative influences of wind, salinity, and temperature on mixed layer shoaling. We observe that wind plays the most significant role in mixed layer shoaling, followed by temperature and salinity. The boreal summer intraseasonal oscillation induced wind relaxation, increased shortwave radiation, and freshwater influx lead sea surface temperature by 7, 5, and 4 days, respectively. Importantly, mixed layer shoaling leads SST anomalies by 1–2 days. Therefore, the current study also suggests an intraseasonal predictability source for NECS‐SYS MHWs.