Khadori power station in Georgia with a transbasin diversion system take water from two rivers. The two branch tunnels have different length, which confluence into main tunnel. This paper analyses characteristics of the diversion system, such as different water level of upstream, different length of branch tunnel and complex flow at branch tunnel junction. Numerical simulation is set up by the method of characteristics. It solves the highest and the lowest water level of fluctuating in surge chamber at the most disadvantagous conditions. The results of numerical simulation are similar to which of model tests.The numerical simulation model set up in this paper is conducive to develop power station with the transbasin diversion system.