In order to find some effective management policy by the feedback loops analysis of a complex system, we transformed the rate variable fundamental in-tree model of SD to a diagonal-0 branch-vector matrix using the method combining graph theory and algebra to work out there are how many newly gained feedback loops in a SD model when a new management activity was introduced into. We created a SD model of a human resource management in an organization, and using this new method, we proved that there were 16 positive and 17 negative newly gained feedback loops by introducing a new HR management of grade-salary incitement on performance level. We proved that the grade-salary-incitement improved the organizational performance, but on the other hand, it restrained the performance of the organization because of the increasing cost. By analyze the growth limited structure model, we find the policy of using the grade-salary-incitement to increase the performance of both the employees and the organization better.