The invention discloses a code morphing-based binary code obfuscation method. The method comprises the following steps: 1, determining a morphing template library; 2, detecting a PE (Portable Execute) file; 3, locating a key code segment; 4, disassembling the key code segment to obtain an assembly instruction sequence, identifying a circular structure in the code segment, and calculating the weight of each instruction in the key code segment; 5, morphing all assembly instructions in the assembly instruction sequence; 6, slicing the assembly instruction sequence and re-sequencing; 7, assembling a new assembly instruction sequence generated in the step 6, and converting into a binary code; 8, reconstructing the PE file. In the method, a computer system is used for obfuscating the executable binary code file under a windows system, so that high protection strength is achieved, and extension becomes easy.