This paper presents an algorithm that combines the chaos optimization algorithm with the maximum entropy(COA-ME)by using entropy model based on chaos algorithm,in which the maximum entropy is used as the second method of searching the excellent solution.The search direction is improved by chaos optimization algorithm and realizes the selective acceptance of wrong solution.The experimental result shows that the presented algorithm can be used in the partitioning of hardware/software of reconfigurable system.It effectively reduces the local extremum problem,and search speed as well as performance of partitioning is improved.