The Heihe River is the second longest inland river in China, which is one of the most important inland river basins in the northwest area. The effect of drought on ecological environment can be exacerbated by climate change. Eco-water diversion project was implemented since 2000 to solve the increasingly serious problem of ecological environment deterioration in the lower reaches of Heihe River Basin. In order to reveal whether the eco-water diversion project solve the ecological environment deterioration thoroughly, the change of hydrology and vegetation were investigated and compared by using the remote sensing data, field surveys, monitoring and statistics data. Our results showed that the soil water content, groundwater level and vegetation coverage increased after eco-water diversion, especially in 0-20cm, the value increased 30.05%, which results vegetation restoration in some area. However, the seasonal distribution of eco-water diversion is extremely uneven, 70% of the runoff is mainly concentrated in January to March, and September to October. Water was seriously insufficient in the critical water demand period of plants such as germination and fruit period due to river cutout. Moreover, some areas were degraded due to salinization. In addition, the extreme change of soil water is not conducive to plant growth, but will increase the waste of water resources due to the increasing of ineffective surface evaporation. It is difficult to improve the quantity of discharged water in the upper reaches of Heihe River, so the distribution time and mode is very important for stable and healthy development of vegetation in the downstream. Therefore, eco-water diversion project is not a simply measure to improve the ecological environment. We suggested that hydrological processes should be consistent with ecological processes in the lower reaches of Heihe River, otherwise, the most important significance of eco-water diversion project will be lost. Exploring this will be helpful in formulate scientific and reasonable water dispatching scheme, achieve water resources allocation and water demand matching, improve ecological benefits.