The hydrogeological conditions in the Junggar Basin from the deep to the shallow potion were obviously different, and there were various hydrochemical sections. High salinity CaCl2 water was in the deep, lower salinity CaCl2 water in the shallow, and the lower to high salinity NaHCO3 water in the middle. The distribution of different water types in the section was considered to be in close association with the lurk thrust fault in the deep and the normal fault in the middle section. The section could be divided into three hydrogeological gyrations, and each gyration had different hydrochemical characteristics and formed different hydrochemical sections. The evolution of hydrodynamics had close relation with hydrocarbon migration and accumulation. The flow directions in the Carboniferous to Triassic were from northwest to southeast and from southwest to northeast, whereas the main flow direction was from southwest to northeast in the Juro-Cretaceous.