Water header is the most common structure in the design of flow system for energy and power system. The complex flow structure could result in some problems when CFD simulation is applied in the whole system analysis. The rapid change in velocity distribution of the flow field leads to difficulties to create suitable boundary-layer mesh, and the complex flow structure will also make residuals hard to reach convergence criteria. Large eddy simulation is promising to promote these studies, it is more accurate than RANS method and can capture many non-steady-state characteristics those RANS method cannot obtain. In this study a typical water header flow structure is investigated by RANS and large eddy simulation methods. By comparing the detailed flow structures in the results of two methods, the deficiency of RANS method was found. The results of large eddy simulation can be used to guide the establishment of meshes and the application of time-averaged turbulence models to improve efficiency in engineering. The asymmetric Reynolds stresses may induce asymmetric flow field in symmetric geometry.