Static Volume method is generally introduced into flow meters, the method is based on steady flow and has some limitations such as uncertainty of measurement results. To study the uncertainty of variable waterhead reservoir in the process of vortex generation and evolution of free surface, large eddy simulation and volume of fluid are introduced into simulating the process of the presence of vortex in a variable waterhead reservoir using the numerical software platform Ansys Workbench FLUENT. According to the flow characteristics, four typical stages of the developing process were selected, and the regularities of the radial velocity, tangential velocity and axial velocity of B-type and D-type free surface vortex along the direction of radial were mainly analyzed. The numerical simulation results show that the vortexs gather towards the center causing the free surface to depress and eventually become vortex and when the water level drops to about 21.4% of the height of the variable waterhead reservoir, the free surface begins to appear depressed.