The allocation process of HEIs’(Higher Education Institutes) resources is divided into macro, mid and microlevel. Regarding the government’s resources and the social resources as the external environment factors, and taking the allocation of the resources of school subordinate units and departments for the important aspect of the allocation of the whole resources, it is studied that the allocation the financial and material resources, especially the financial resources, of HEIs’ resources at mid and microlevel from the point of school view. Under the direction of scientific development view, it is proposed that the guiding ideology, basic principle and certain significant relations, which need to be well dealt, the mechanism and the specific ways: total budget management, as well as the corresponding security measures for optimizing the allocation of HEIs’ resources.