Aiming at the simple obfuscating result of the existing control flow obfuscating algorithm, an obfuscating algorithm based on congruence equation and improved flat control flow was presented. First of all, a kind of opaque predicate used in the basic block of the source code was created by using secret keys and a group of congruence equation. Then, a new algorithm for creating N-state opaque predicate was presented based on Logistic chaotic mapping. The proposed algorithm was applied to the existing flat control flow algorithm for improving it. Finally, according to the combination of the above two proposed algorithms for obfuscating the source code, the complexity of the flat control flow in the code was increased and make it more difficult to be cracked. Compared with the flat control flow algorithm based on chaotic opaque predicate, the code's tamper-proof attack time of the obfuscated code was increased by above 22% on average and its code's total cyclomatic complexity was improved by above 34% on average by using the proposed obfuscating algorithm. The experimental results show that, the proposed algorithm can guarantee the correctness of execution result of the obfuscated program and has a high cyclomatic complexity, so it can effectively resist static and dynamic attacks.