The outburst of Zhuonai Lake (ZL) in 2011 changed the local hydro-ecological system in northeast Hoh Xil (HX). This study focuses on the impact of the outburst on lake water storage changes (LWSCs) of four lakes in this region. Monthly LWSC from 2009 to 2016 were constructed using Landsat and Cryosat-2 data. We determined and validated lake levels and areas derived from Cryosat-2 and Landsat data, respectively. The two satellite-derived sequences were merged by interpolation to compute LWSC, based on the level-area curve derived from the digital elevation model (DEM). Results reveal the apparent impact of the outburst on the hydrological system. Before the outburst, water volumes in all four lakes continuously grew from January 2009 to September 2011, with a total increase of 1.49 ± 0.08 Gt. Most increased water was distributed in ZL and Kusai Lake (KL). The LWSC of each lake was strongly correlated (>0.9) with those of the whole basin. However, from October 2011 to December 2016, there was no ascending trend in LWSC of the three upper stream lakes, although the water volume in the basin was still increasing. More than 80% of the increased water flowed into Salt Lake (SL). Only the LWSC of SL kept a high correlation (0.91) with those of the whole basin.