The relationship between hydrological alteration and climate variability in the upper Yangtze River is not fully understood. In this paper, the periodicity features and the intercorrelation of annual and seasonal eco-flow metrics at the Yichang gauge station are analyzed for the period 1882 to 2013. Analysis is carried out to explore the formation of the eco-flow metrics and the possible linkages between eco-flow metrics and selected climate indices, using the cross-wavelet and wavelet coherence methods on data from 1948 to 2013. The results show that the variation of eco-flow metrics correlates well with some selected climate indices, but changes in different eco-flow metrics are complex. Most annual and seasonal eco-flow metrics correlate well with the Northern Hemisphere (N.H) and Indian Ocean Dipole (IOD) and have a significant common power in the two to four years band. In addition, most annual eco-flow metrics have an obvious phase relationship with the selected climate indices. However, the seasonal eco-flow metrics have no significant phase relationship with the selected climate indices. These findings provide a better understanding of how hydrological alterations of the streamflow and better water resource management can ensure ecosystem sustainability for the Yangtze River.