Combined analyses of deep tow magnetic anomalies and International Ocean Discovery Program Expedition 349 cores show that initial seafloor spreading started around 33 Ma in the northeastern South China Sea (SCS), but varied slightly by 1–2 Myr along the northern continent‐ocean boundary (COB). A southward ridge jump of ∼20 km occurred around 23.6 Ma in the East Subbasin; this timing also slightly varied along the ridge and was coeval to the onset of seafloor spreading in the Southwest Subbasin, which propagated for about 400 km southwestward from ∼23.6 to ∼21.5 Ma. The terminal age of seafloor spreading is ∼15 Ma in the East Subbasin and ∼16 Ma in the Southwest Subbasin. The full spreading rate in the East Subbasin varied largely from ∼20 to ∼80 km/Myr, but mostly decreased with time except for the period between ∼26.0 Ma and the ridge jump (∼23.6 Ma), within which the rate was the fastest at ∼70 km/Myr on average. The spreading rates are not correlated, in most cases, to magnetic anomaly amplitudes that reflect basement magnetization contrasts. Shipboard magnetic measurements reveal at least one magnetic reversal in the top 100 m of basaltic layers, in addition to large vertical intensity variations. These complexities are caused by late‐stage lava flows that are magnetized in a different polarity from the primary basaltic layer emplaced during the main phase of crustal accretion. Deep tow magnetic modeling also reveals this smearing in basement magnetizations by incorporating a contamination coefficient of 0.5, which partly alleviates the problem of assuming a magnetic blocking model of constant thickness and uniform magnetization. The primary contribution to magnetic anomalies of the SCS is not in the top 100 m of the igneous basement. Key Points: Deep tow magnetics and IODP Expedition 349 constrained opening history Variations are observed in spreading rate and onset of drifting and ridge jump Magnetic anomalies are not primarily sourced from the top 100 m of the basement