The response of vegetation to climate at different scales provides synthetic understandings of environmental changes. In this paper, the spatio-temporal variation of the vegetation and its relationship with climatic factors in the Bosten Lake Basin was studied based on MODIS NDVI dataset. The correlation and time lag between the NDVI (16-day NDVI and cumulative NDVI in growing season) and the climate factors (air temperature, precipitation, sunshine duration and relative humidity) were investigated during 2001-2016. The results show that:(1) The cumulative NDVI in growing season exhibited an increasing trend by 0.014 a^-1. The most significant increasing areas are mainly located in the lower edge of permafrost belts and the new irrigated farmland areas. (2) The interannual variation of vegetation cover was strongly related with the water conditions. The significant correlation between 16-day NDVI and the climate factors had highlighted the significant impacts from temperature and lower correlation with precipitation, which indicated that the short-term growth of vegetation is mainly sensitive to thermal conditions. (3) The time lag correlation between 16-day NDVI and the climate factors showed that vegetation had different time-lag effects on climate change during different growth stages. There was a 0.5-1 month time lag effect on temperature during the early and late stages of the growing seasons. However, the most significant effect during the fast growing seasons was the 0.5-3 month time lag on precipitation. This difference revealed the mechanism rhythms of hydrothermal conditions on the vegetation growth at different stages.