Turpan basin is an important coal base in China, and studying the regional groundwater flow system is of great significance for regional water resources research. The well depths of the sampling points are mainly concentrated in more than 100 meters and less than 30 meters. All the samples can be divided into four groups based on the well depth,and in combination with the elevation effect of the isotope value and the locations of the sampling points, the nearby points are grouped into the same water system. An analysis shows that the north of the volcanic rocks belongs to the same type of groundwater flow system,while the water system in the south of the volcanic rock exhibits features of multistage flow system because of the reservoir building, the continuous improvement of the water conservancy facilities and the reformation of agricultural irrigation system; its forming condition is mainly influenced by natural and human activities. The isotope and TDS values of T1 point are higher, so it might have been the edge of the Aydingkol Lake, and the lake water level was shallow and isotope evaporation effect was obvious at that time. At the same time, loopholes were existent in the bedrock, the groundwater could flow from the north to the south of the basin.