The operation mode of reservoir is one of the factors that can be controlled by human, and it will cause hydrology and heat changes in the river. The water temperature characteristics of different operation methods were analyzed based on the measured data and simulation results by taking two different types of regulation reservoirs as an example. The result indicated that when multi-year regulating reservoir running on a high-water level in the flood season of the dry year, there would be a stable three-layer of vertical water temperature phenomenon and small changes on the bottom cryosphere, also an obviously flat phenomenon of the discharged water temperature thoroughly changed the sine distribution rule of natural water varying with the season. The vertical temperature of reservoir was mixed distribution in the dry season and dual stratification distribution in the flood season without cryosphere in bottom when the reservoir running on a lower water level in the average year. Meanwhile, the discharged water had little impact on the down-stream river water temperature. Moreover, the effects on water temperature are between the former two while the reservoir running on a middle-water level of the flood year. As to the multi-year regulating reservoir, there were little differences on water temperature distribution in the flood year or the average year, but an obviously delay of the discharged water temperature in the warming up time of the dry year. Therefore, different operation modes should be taken into consideration and the negative effect of cold water can be avoided by setting the reservoir on an appropriate operation mode.