This study investigates the origin and causes of the prominent subsurface temperature warming in the southern Bay of Bengal (BOB) during boreal-summer (July to September). Using data from the Array for Real-time Geostrophic Oceanography and a 1.5-layer reduced gravity model, we identify significant spatial variation in this warming as it interacts with the fluctuating thermocline. Simulation results indicated that the combined effects of distinct phase-locking from both local and equatorial remote forcing in the BOB modulated the anomalous deepened thermocline in forming two unique stages during the evolution of the subsurface warming. In the formation stage, the remote-forced Rossby waves reflected from the eastern boundary and the local-forced Rossby waves induced by local negative wind stress curl together deepen the thermocline in the southern BOB, resulting in warming across the southern BOB in June. In the maintenance stage, the local-forced Rossby waves sustain while the equatorial signals shift into negative phase, which shoaling the eastern thermocline of the southern BOB, results in accentuating the warming primarily in the west. Causes of these different stages are as follows: the semiannual remote-forced Rossby wave and annual local-forced Rossby wave interfere constructively in causing the basin-scale warming in the early boreal summer, while the remote-forced Rossby wave turns to negative phase and interferes destructively with the positive local-forced Rossby wave from July to September, result in the only sustaining warming in the western BOB. This study highlights the complex interactions between annual and semiannual Rossby waves in the subsurface temperature variability and provides insights to enhance subsurface forecasting in the southern BOB.