Acoustic tomographic inversion is based on travel times measured along the transmission paths between all station pairs to reconstruct three-dimensional temperature structures with mesoscale anomalies. In this study, tomographic simulation experiments were designed based on the Hybrid Coordinate Ocean Model (HYCOM) reanalysis data to reconstruct mesoscale phenomena from travel time data obtained from five, seven, and nine stations in the South China Sea over a domain of 100 × 100 km. The travel times for each station pair were calculated in the vertical section using the Bellhop acoustic ray simulation method. Six Empirical orthogonal function (EOF) modes of sound speed along the sound transmission paths in a vertical slice were used to formulate the inversion equations. The horizontal-slice distributions of temperature in the tomography domain were reconstructed using the grid-segmented method for each depth layer. For station-to-station distances greater than 100 km, the performance of inversion was best for the seven-station case rather than for the nine-station case, with the highest horizontal resolution of the three cases. This case study concluded that the seven-station case rather than the nine-station case provided an optimal station number for reconstructing the three-dimensional temperature fields.