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Satellite-borne embedded systems require the properties of low-powered and reliability in the spatial radiation environment. The control flow checking is an effective way for the running systems to prevent the broken-down caused by Single Event Upsets. Traditional software control flow checking uses a great deal of branch instructions to detect errors, thus brings great overhead in power dissipation. In this paper, a partition method of basic block is suggested. In this partition method, branch instructions are reduced greatly, while the high error detection coverage remain ensure. The simulated results show that compared with the traditional Control Flow Checking by Software Signatures(CFCSS) control flow checking algorithm, the Improved algorithm can reduce total branch instructions by over 10%, reduce the power dissipation by nearly 9%, without decreasing the error detection coverage.