In Turpan Basin, groundwater recharge and discharge system have been sharply changed due to excessive diversion of surface water and overexploitation of groundwater, so a series of ecological environment problems have been caused, such as Aydingkol Lake ecosystem deterioration, Karez flow attenuation and even drying up, land desertification, frequent sandstorm. Karez is an impressive hydraulic engineering project as well as a cultural achievement for over 2000 years. In order to preserve and revitalize some Karezes, multiple measures have been implemented. Based on the data of water use and groundwater evaluation in different period, groundwater budget was calculated, the evolution of groundwater recharge and discharge was analyzed, and the evolution stage was divided according to the variation curve over time. The relationship between groundwater system evolution and Karez flow attenuation was also analyzed using correlation analysis method. The results showed that: 1) Groundwater recharge and discharge were mainly affected by human activities. Annual rainfall was small and slightly showed a trend of decrease, and rainfall infiltration was negligible. The impact of climate change on groundwater system was negligible. River runoff increased slightly. But the river leakage decreased by around 1.0*10~8 m~3 from 1956 to 2014. Channel leakage and field infiltration showed a trend of increase before 1990, reached the peak value of 0.359*10~8 and 0.168*10~8 m~3 respectively, and then declined. Groundwater exploitation by well has experienced sustained increasing, reached the maximum of 3.536*10~8 m~3 in 2010, and declined since 2011, and well production was 2.570*10~8 m~3 in 2014. Karez flow increased in 1960s to the maximum value of 2.173*10~8 m~3, and after that decreased and drying up; only a flow yield of 0.5944*10~8 m~3 was still provided to irrigation in 2014. Spring water, as well as Karez flow, reduced from 1.063*10~8 m~3 in 1958 to 0.0686*10~8 m~3 in 2010. The evaporation discharge of phreatic water decreased from 0.938*10~8 m~3 in 1958 to 0.056*10~8 m~3 in 2011. 2) The correlation coefficients between Karez flow and river leakage, channel seepage, field infiltration, and well water production were 0.373, -0.327, -0.574 and -0.959 respectively. That was to say, Karez flow attenuation was mainly affected by pumping wells, followed by field infiltration, and lastly affected by river leakage and canal seepage. The response relationship between groundwater recharge and discharge system evolution and Karez flow attenuation was decided by their spatial distribution location. In north basin, Karez system was mainly located within the areas with a width of 5.0 km north of the ground water exposure belt, at a distance of 20.0-30.0 km from the river outlet. River leakage and channel seepage were distributed into vast aquifer with an area of 2 000 km~2 in the piedmont Gobi gravel, which caused a small variation of groundwater level. Its influence is limited for most of Karez flow. Although pumping wells were located in the downstream of Karez canal, exploitation made groundwater level sharply decline and had a great influence on Karez flow. In south basin, Karez system was distributed throughout irrigation area, as well as pumping wells, exploiting groundwater caused most Karezes to be dried up and abandoned; only several Karezes located in the edge of irrigation area were still flowing. Field infiltration affected Karez flow significantly due to recharge directly. 3) The abrupt change point of groundwater recharge and discharge was consistent with the implementation stage of national major policy. Policy was a key factor in human factors. Before 1949, only Karez flow and spring water were diverted for irrigation and domestic purposes.