Trend analysis of streamflow provides practical information for better management of water resources on the eve of climate change. Thus, the objective of this study is to evaluate the presence of possible trends in the annual, seasonal, maximum, and minimum flow of Yangtze River at Cuntan and Zhutuo stations in China for the period 1980 to 2015. The assessment was carried out using the Mann–Kendall trend test, and the innovative trend analysis, while Sen’s slope is used to estimate the magnitude of the changes. The results of the study revealed that there were increasing and decreasing trends at Cuntan and Zhutuo stations in different months. The mean annual flow was found to decrease at a rate of −26.76 m3/s and −17.37 m3/s at both stations. The minimum flow was found to significantly increase at a rate of 30.57 m3/s and 16.37 m3/s, at a 95% level of confidence. Maximum annual flows showed an increasing trend in both regions of the Yangtze River. On the seasonal scale, the results showed that stations are more sensitive to seasonal flow variability suggesting a probable flooding aggravation. The winter season showed an increasing flow trend, while summer showed a decreasing trend. The spring flow was found to have an increasing trend by the Mann–Kendall test at both stations, but in the Zhutuo Station, a decreasing trend was found by way of the innovative trend analysis method. However, the autumn flow indicated a decreasing trend over the region by the Mann–Kendall (MK) test at both stations while it had an increasing trend in Cuntan by the innovative trend analysis method. The result showed nonstationary increasing and decreasing flow trends over the region. Innovative trend analysis method has the advantage of detecting the sub-trends in the flow time series because of its ability to present the results in graphical format. The results of the study indicate that decreasing trends may create water scarcity if proper adaptation measures are not taken.