Abstract: In scale of fuel element level in the reactor core, the enthalpy conservation equation and momentum conservation equation are solved by using the structured mesh manner of according matrix algorithm in the sub-channel analysis code named CORTH. At present, parallel computing is introduced to enhance the calculation efficiency of CORTH. The coefficient matrix is with sparse symmetry which can be studied by converting to the undirected graph and using partitioning algorithms to achieve the goal of minimizing the communication volume, computation and load balance. Usually the problem is related to the non-linear polynomial（NP） algorithm. Several typical undirected graph partitioning methods and their effects are compared and discussed under sub-channel analysis scenario. Numerical experiments show that the sub-optimal solution of according matrices could be obtained by multi-level k-way undirected graph partitioning method in the application scenarios based on these algorithms. Furthermore, the computing performance of cluster is carried out for the test of pressure water reactor（PWR） full core sub-channel problem, and the parallel capability is well.