An ocean acoustic tomography (OAT) experiment conducted in the northern South China Sea in 2021 measured a month-long record of acoustic travel times along paths of over one hundred kilometers in range. A mesoscale eddy passed through the experimental region during the deployment of four acoustic moorings, providing unique OAT data for examining the deep temperature change in the eddy and for comparison with the Hybrid Coordinate Ocean Model (HYCOM) data. The existence of the eddy is first confirmed by the merged sea level anomaly (MSLA) image and HYCOM data and it can exceed the depth of the sound channel axis. The temperature changes measured by temperature and depth (TD)/conductivity–temperature–depth (CTD) loggers and by the OAT sound speed are in accordance with those reflected on the MSLA image during the movement of the eddy. However, the eddy movement prompted by temperature changes in the HYCOM data is different from that measured by TD/CTD. The modeled eddy intensity is at least two times less than the measured eddy intensity. At the sound channel axis depth, a factor of approximately 4.17 ms−1 °C−1 can be used to scale between sound speed and temperature. The transmission/reception path-averaged temperature of the eddy derived from the OAT-computed sound speed at the depth of the sound channel axis is five times greater than those in the HYCOM data. OAT is feasible as a tool to study mesoscale eddy properties in the deep ocean, while HYCOM data are not accurate enough for this mesoscale eddy at the sound channel axis depth. It is suggested that the model be refined by the OAT path-averaged temperature as constraints when the HYCOM data capture the mesoscale eddies.