Tropical cyclones (TCs) induce heat pump and cold suction in the upper ocean layer. However, limited research investigated whether this heat can be effectively transported into the deep ocean. The present study shows that seawater at Station S2 is anomalously warmer in the deep ocean layer than at S1 and S3 during Typhoon Kalmaegi (2014) in the South China Sea. The turbulence‐induced vertical heat flux is estimated based on fine‐scale mixing parameterization but it cannot explain the warming rate below the thermocline. Therefore, a new method is proposed to estimate the vertical velocity, allowing us to calculate the heat flux more accurately. To elucidate the underlying causes of the observed differences, we analyze horizontal velocity to examine the role of mesoscale eddies in modulating near‐inertial waves (NIWs)‐induced vertical heat flux. Station S1 is located inside a cyclonic eddy while S2 and S3 are within two distinct anticyclonic eddies. According to the “Chimney Effect” theory, cyclonic (anticyclonic) eddies tend to limit (enhance) the vertical propagation of the NIWs. While this theory explains the confined heat flux at S1, it fails to explain the differences observed at S2 and S3. Further examination of the vertical structures and intensities of the two anticyclonic eddies reveals that the eddy at S2 extends much deeper and is stronger than that at S3, allowing the NIWs to propagate and transport heat deeper at S2 than at S3. The study demonstrates the role of TC‐induced NIWs in deep ocean heat transport under the influence of mesoscale eddies.

near-inertial waves, heat transfer, mesoscale eddies