Semi-enclosed bays subject to intensive thermal discharges present significant challenges in quantifying cumulative thermal effects and assessing thermal environmental carrying capacity. Taking Daya Bay as the study site, this paper develops a two-dimensional hydrodynamic–thermal coupling model using MIKE 21 FM to simulate the spatially integrated temperature rise field induced by four thermal discharge sources under a worst-case hydro-meteorological scenario—characterized by neap tide conditions and a low wind speed of 1.5 m/s. Model performance is rigorously validated against in situ monitoring data and Landsat-derived sea surface temperature observations. Building upon this validated simulation framework, the thermal environmental carrying capacity is quantified via the contour-constraint method, and the spatial compatibility between the simulated temperature-rise contours and designated marine functional zones is systematically evaluated. Results show the following: (1) Intake recirculation significantly reduces the effective thermal load discharged into the bay, and the 1 °C temperature-rise envelope is reduced by 49.2% after intake flow correction. (2) Under the benchmark parameter, the bay-scale thermal environmental capacity utilization rate is 90.7% with approximately 2000 MW residual capacity, and the comprehensive uncertainty range is ±13% to ±17% considering parameter sensitivity. (3) The 1 °C temperature-rise contour overlaps with the core protected area by about 8.7 km², showing potential spatial conflict with ecological zoning. This study offers technical support for optimizing the spatial layout of thermal discharges and implementing total load control in semi-enclosed bays.