Abstract: This paper designes in the environment of the heterogeneous multi-core architecture of reconfigurable Computing，using the C/C++ function pointer，with which everyone is familiar，and according to the results of hardware and software defragmentation，programmers accomplished the dynamic connection of the software or hardware function. At the same time，getting the frequency of each function，combining with its running time and hardware space and so on，and using the pre-configuration algorithm，the running time of all functions will be shortened and the speed of computing will be accelerated，then the overhead of reconfiguration will be reduced.