In the current, Multi-core CPU has become the general configuration of the PC. In order to give full play to the performance of the PC and improve the running speed of application software, how to parallel computing on the multi-core CPU is studied in this paper. The research is applied into the calculation of shallow water flow velocity measurement model with virtual boundary condition. The test result showed that the running speed on dual-core CPU and on quad-core CPU is 1.4 times and 2.3 times faster than that on the single-core CPU, which indicates the more the number of cores, the greater the multiplies.