The headwaters of the Yangtze River are located on the Qinghai Tibetan Plateau, which is affected by climate change. Here, treamflow trends for Tuotuohe and Zhimenda sub-basins and relations to temperature and precipitation trends during 1961–2015 were investigated. The modified Mann–Kendall trend test, Pettitt test, wavelet analysis, and multivariate correlation analysis was deployed for this purpose. The temperature and precipitation significantly increased for each sub-basin, and the temperature increase was more significant in Tuotuohe sub-basin as compared to the Zhimenda sub-basin. A statistically significant periodicity of 2–4 years was observed for both sub-basins in different time spans. Higher flow periodicities for Tuotuohe and Zhimenda sub-basin were found after 1991 and 2004, respectively, which indicates that these are the change years of trends in streamflows. The influence of temperature on streamflow is more substantial in Tuotuohe sub-basin, which will ultimately impact the melting of glaciers and snowmelt runoff in this sub-basin. Precipitation plays a more critical role in the Zhimenda streamflow. Precipitation and temperature changes in the headwaters of the Yangtze River will change the streamflow variability, which will ultimately impact the hydropower supply and water resources of the Yangtze Basin. This study contributes to the understanding of the dynamics of the hydrological cycle and may lead to better hydrologic system modeling for downstream water resource developments.