The hydrological system is composed by subsystems, and affected by the interaction of multi factors, multi scale, which result in interaction structure of more complex produced in time and space and formed a great complex system.So it has also caused more attention by scholars to use complex network theory to study hydrological problem of. This paper first analyzed the complexity of hydrological system, and introduced the related knowledge of complex network. Then it summarized some applications in hydrological research which included analysing hydrological process by using the statistical properties of complex networks;realizing watershed delineation by using complex network's community mining algorithm;optimizing hydrological monitoring network by using the evaluation of node's importance. Finally,the paper prospected the new direction to resolve other problems in hydrological system with complex networks.