Based on the content of Ba and ratio method of Sr/Ba in sediment, this paper makes qualitative analysis of sedimentary water body salinity of Carboniferous period in the northeast margin of Junggar basin. On this basis, and combing with the content of clay mineral in fine clastic rocks, we make quantitative calculation of the salinity of ancient water body, and the results show that, in early Carboniferous the ancient sedimentary water body was brackish water to salt water, while in late Carboniferous it was fresh water. Furthermore, the salinity of ancient water body in Carboniferous is far lower than normal salinity of sea water. Comprehensive analysis shows that the northeast margin of Junggar basin was generally located in the margin of continental in Carboniferous. In the early Carboniferous, the sedimentary background of northeast margin was arc-back arc basin and divided by many arcs in plane, as a result, the salinity changed considerably; while in the late Carboniferous, influenced by regional tectonic setting, this area was lifted and became land, and the salinity was decreased in general. Depth analysis of ancient water salinity will have a profound understanding and significance to the Carboniferous tectonic paleogeography and hydrocarbon exploration.