Water temperature is a major driver of riverine ecosystems and has an extremely significant impact on them. Understanding the multi-scale water temperature dynamics in a river basin is critical to analyze the water temperature status of rivers. In this study, the intra-annual and inter-annual time series of water temperature (WT) at Yichang station in the middle reaches of the Yangtze River over the past 62 years was analyzed using complex Morlet wavelet functions to reveal the complex structure of water temperature variation at multiple time scales. The ecological impact of water temperature changes on the reproduction of the “Four Major Chinese Carp” under the influence of the Three Gorges Dam (TGD). The results showed that the water temperature at Yichang Station has a multi-level time scale structure, with an increasing trend at the inter-annual scale from 1956 to 2017, but different variations at the seasonal scale, and the water temperature cycles at both the inter-annual and seasonal scales have time scale variations of about 8–14 years and 4–7 years, with obvious characteristics of WT variation stages. The inter-annual and summer scales will have low WT in 2017–2022 and high WT in 2023–2027, while the other seasonal scales will have high WT in the next few years, either in the short or medium term. The correlation between air temperature and WT is the most significant among the three drivers of air temperature, flow and rainfall, and the correlation between WT and the air temperature is the most significant in winter scale under the influence of the Three Gorges Dam construction. Since the completion of TGD in 2003, the summer drainage temperature has decreased and the breeding period of the “Four Major Chinese Carp” has been shortened by 30–40 days compared to that before the construction of TGD. The results of this study can be used as a basis for further exploration of the formation mechanism of river water temperature and provide a scientific basis for river ecological protection.