This paper proposes a approach to manage internal hardware resources of FPGA reconfiguration system. System based on user’s requirements in accordance with existing hardware resources, flexibly do configuration or reconfiguration. When a new task arrives, we must consider the overall resources to the system consumed, to determine whether the implementation. In this way we consider each functional units in the system, remaining resources are enough or not enough to supply a new task to use, after comparisons we can decide to do configuration or reconfiguration. The proposed algorithm is validated on Xilinx ISE 9.2i platform, and C/C++ program.