Abstract: The two-level management is engaged in exploration in the secondary distribution management system. Based on published papers and performance evaluation results in each school in colleges and universities, the secondary level schools in colleges and universities were divided into golden cows, stars, problems, and skinny dogs by Boston matrix. According to characteristics of different schools of colleges and universities, future development patterns were classified into sustaining pattern, developing pattern and remedy pattern. In different patterns, aiming at maintaining the status quo and developing four kinds of schools respectively, long-term development strategy was put forward. In the view of the whole development plan, development patterns like stars and problems were chosen and developed which were based on maximizing the distribution of benefits in colleges and universities in principle. Each input index to every secondary school was adjusted to achieve partial and effective resources distribution in colleges and universities. The research emphasized that the two-level management must be based on the evaluation of the schools' performance to allocate teaching, scientific research, personnel, and financial resources, thus the resources allocation of two-level management is relatively fair and effective.