The establishment and operation of cascade reservoirs in the mainstream of the upper and middle reaches of the Yangtze River have changed the river’s thermal regimes. This study analyzed the correlation between water temperature and its influencing factors and employed various evaluation indexes—including ∆T (the temperature-increasing index, °C/100 km), IEC (the extreme fluctuation index), IBD (the baseline deviation index), and IPO (the phase offset time index). The aim was to uncover the variation characteristics and influencing factors of water temperature and quantify the impact of cascade reservoir construction on annual and seasonal water temperature rhythms. Our findings show that the construction and operation of cascade reservoirs weaken the synchronization of water temperature and air temperature downstream. The construction and operation of cascade reservoirs in the middle and lower reaches of the Jinsha River led to obvious homogenization, baseline deviation, and lagging effects on water temperature downstream, which intensified with the increase in storage capacity. These effects were more pronounced in colder months compared to warmer months. Additionally, the influence of tributaries and water–air heat exchange on these effects is alleviated to different degrees. These results are significant for assessing river ecological health in the context of cascade hydropower development.