Because of the Lack of water resources and the increasing water quantity used in living and production, the water resources are becoming the restrictive factor of regional economic and social development in in Manas river basin. The exploitation and utilization of conventional water resources has reached more than 95% in the basin,it caused great attention that the development and utilization of non-conventional water resources for agricultural development and ecological environment construction. At present, the exploitation and utilization of the non-conventional water resources(shallow underground salt water，saline water) for agriculture and forestry has become more and more widespread and in-depth. because of the lack of scientific instruction and reasonable exploitation, which not only caused water level falling, leading to degradation of the brittle natural entironment, but also caused SBHCSS and the decline in productivity. With the analysis of the non-conventional water resources actual exploitation and utilization, under the scientific development concept, the aryicle puts forward the sustained strategies of non-conventional underground water resources (salt water, saline water) reasonable exploitation and the irrigation return flow reuse efficient exploitation which is used for ecological restoration and reconstruction.