Turbulence-enhanced mixing of upper ocean heat allows interaction between the tropical atmosphere and cold water masses that impact climate at higher latitudes thereby regulating air-sea coupling and poleward heat transport. Tropical cyclones (TCs) can drastically enhance upper ocean mixing and generate powerful near-inertial internal waves (NIWs) that propagate down into the deep ocean. Globally, downward mixing of heat during TC passage causes warming in the seasonal thermocline and pumps 0.15 to 0.6 PW of heat into the unventilated ocean. The final distribution of excess heat contributed by TCs is needed to understand subsequent consequences for climate; however, it is not well constrained by current observations. Notably, whether or not excess heat supplied by TCs penetrates deep enough to be kept in the ocean beyond the winter season is a matter of debate. Here, we show that NIWs generated by TCs drive thermocline mixing weeks after TC passage and thus greatly deepen the extent of downward heat transfer induced by TCs. Microstructure measurements of the turbulent diffusivity ([Formula: see text]) and turbulent heat flux (J[Formula: see text]) in the Western Pacific before and after the passage of three TCs indicate that mean thermocline values of [Formula: see text] and J[Formula: see text] increased by factors of 2 to 7 and 2 to 4 (95% confidence level), respectively, after TC passage. Excess mixing is shown to be associated with the vertical shear of NIWs, demonstrating that studies of TC-climate interactions ought to represent NIWs and their mixing to accurately capture TC effects on background ocean stratification and climate.