The invention discloses a control flow complication-based Java code obfuscation method. The method comprises the steps of 1, constructing a non-transparent predicate set; 2, discovering a loop structure; 3, separating the loop structure; 4, inserting the non-transparent predicate set into the separated loop structure; and 5, complicating the loop structure. According to the method, the shortcoming of insufficient utilization of the loop structure in an existing code obfuscation method is overcome and a control flow complication method utilizing the loop structure is realized.