The spatio temporal variation characteristics of groundwater depth and the inflow of river and its ecological effect were studied based on the monitoring of hydrological and ecological parameters in the main stream area of Tarim River in recent 20 years.The results showed that the annual variation of ground water depth in the upper and middle reaches of the main Tarim River was 0.42~0.92 m in the dry season from March to April, and 1.06~3.67 m in the flood season from July to September. After nearly 20 years of ecological water conveyance, the groundwater depth in the downstream section had increased by 3.75 m during 2009-2017. The depth of groundwater varied significantly with the amount of water conveyance. Generally, it reached the peak value within one month after the water conveyanced. After that, it gradually decreased until the next water conveyance. After 2009, the ecological water transport has obvious effect on the vegetation restoration of downstream, and the average value of NDVI in the downstream increased from 0.05 to 0.15. This study systematically analyzed the comprehensive response of regional ecological environment to groundwater since the ecological transport of the main stream of Tarim River, which could provide theoretical basis for regional water resource management and further quantification of water transport benefits.