To explore the impacts of a moving tropical cyclone (TC) on the deep ocean, a linear continuously stratified model is solved by the method of solving for the temporal and horizontal structure of each vertical mode. The response of the barotropic mode to the TC’s pressure gradient is an isostatic balance, where the sea level rise almost completely cancel the atmospheric low pressure. The response of the barotropic mode to the winds is a permanent sea level drop behind the TC. The horizontal extent of this response is determined by the distribution of the weak negative wind curl outside the core of the strong positive curl. The baroclinic response to the winds is dominated by the well-known train of near-inertial oscillation behind the TC. In addition, there is a mean upwelling and a resultant cooling. The lateral scale of the first upwelling behind the TC is determined by the size of the TC’s positive curl core; further behind in the TC’s wake, this feature spreads laterally at the group speed of inertio-gravity waves for the mode. The three-dimensional structure is then constructed by superposing these vertical modes. The position of the first upwelling peak coincides between the baroclinic modes; this alignment results in a vertical column of upwelling. Further down the wake, this coherence is gradually lost because of slight difference in the streamwise wavelength between modes. Also, lower vertical modes dominate further away from the TC track because of faster lower modes. A uniform-density ocean shows a similar columnar upwelling and downwelling pattern as a response to the same wind curl. The pressure anomaly field at the ocean bottom is dominated by the barotropic response to winds, modified by the baroclinic response. The near-inertial oscillation reaches the bottom quickly because of the columnar response.