Typhoon is a major cause of multiple disasters in coastal regions of East Asia. To advance our understanding of typhoon-ocean interactions and thus to improve the typhoon forecast for the disaster mitigation, two data buoys were deployed in the western North Pacific, which captured Super Typhoon Nepartak (equivalent to Category 5) in July 2016 at distances <20 km from the typhoon's eye center. Here we demonstrate that the unprecedented dataset combined with the modeling results provide new insights into the rapid temperature drop (~1.5 °C in 4 h) and the dramatic strengthening of velocity shear in the mixed layer and below as the driving mechanism for this rapid cooling during the direct influence period of extremely strong winds. The shear instability and associated strong turbulence mixing further deepened the mixed layer to ~120 m. Our buoys also observed that inertial oscillations appeared before the direct wind influence period.