[Objective] As the core water source of the middle route of the South-to-North Water Transfer Project, the spatiotemporal distribution of water temperature in Danjiangkou Reservoir directly affects the aquatic ecological processes and water quality evolution within the reservoir area. This study aims to clarify the spatiotemporal distribution patterns of water temperature in Danjiangkou Reservoir through prototype observations across the entire reservoir, to identify thermal stratification types, and to reveal the factors influencing differences in thermal structure between the Danjiang Reservoir and the Hanjiang Reservoir, thereby providing a scientific basis for reservoir water quality management, ecological protection, and so on. [Methods] In 2023, prototype observations of water temperature were carried out in Danjiangkou Reservoir during four typical hydrological periods, including the dry season (February), the normal flow season (June), and the flood season (September and October). A total of 16 observation sections were deployed throughout the entire reservoir, including one section in front of the dam, seven along the mainstream of the Hanjiang River, and eight along the mainstream of the Danjiang River. Based on the observation data, multiple discriminant methods such as water residence time (T_r), runoff-storage capacity ratio (α), reservoir width-depth ratio (R), and densimetric Froude number (Fr) were comprehensively applied to systematically analyze the thermal stratification structure of the reservoir and its spatiotemporal evolution characteristics, and to further explore the influence mechanisms of meteorological, hydrological, and topographic factors on thermal stratification. [Results] (1) The vertical thermal stratification structure of Danjiangkou Reservoir exhibited a significant seasonal variation pattern: during the dry season (February), the water body was well mixed with no obvious stratification. During the normal flow season (June), stable stratification formed, and increased air temperature and enhanced inflow strengthened vertical mixing of the water body, resulting in a double-thermocline type vertical water temperature structure in the Han Reservoir, with a surface-to-bottom temperature difference of approximately 20 ℃. During the flood seasons (September-October), the thermocline deepened, and thermal stratification was the most stable and exhibited greater thickness. (2) The reservoir’s surface water temperature was highly correlated with air temperature (R²=0.976), whereas variations in middle and bottom water temperatures exhibited a lag, regulated by heat transfer within the water body and hydrological processes. (3) The Dan Reservoir and the Han Reservoir exhibited significantly different hydrological and hydrothermal characteristics. The Han Reservoir had a shorter water residence time (257 days), a larger runoff-storage capacity ratio (α=1.47), and stronger hydrodynamic forcing, exhibiting characteristics of a riverine reservoir. Its thermocline was mainly controlled by inflow dynamics, with isotherms showing an inclined pattern. The Dan Reservoir had a longer water residence time (336 days), a smaller runoff-storage capacity ratio (α=1.04), and slower water flow conditions, showing characteristics of a lacustrine reservoir. Its thermocline was primarily controlled by solar radiation and meteorological conditions, with more horizontally distributed isotherms and a more stable and persistent stratification structure. (4) Operation of the intake in front of the dam had an impact on the local thermal structure, and clustering of isotherms was observed at depths near the intake. [Conclusion] Through systematic prototype observations, this study comprehensively reveals the complex spatiotemporal thermal stratification structure of Danjiangkou Reservoir, particularly confirming the existence of a double thermocline during the normal flow season and the essential differences in stratification mechanisms between the Dan Reservoir and the Han Reservoir. This study innovatively demonstrates that two thermal stratification modes, lacustrine (Danjiang Reservoir) and riverine (Hanjiang Reservoir), coexist within the Danjiangkou Reservoir, providing an important foundation for understanding migration and transformation of nitrogen and phosphorus, algal growth, and seasonal water quality changes in the reservoir area.