Code-injection attacks pose serious threat to today’s Internet. The existing code-injection attack defense methods have some deficiencies on performance overhead and effectiveness. To this end, we propose a method that uses system called randomization to counter code injection attacks based on instruction set randomization idea. System calls must be used when an injected code would perform its actions. By creating randomized system calls of the target process, an attacker who does not know the key to the randomization algorithm will inject code that isn’t randomized like as the target process and is invalid for the corresponding de-randomized module. The injected code would fail to execute without calling system calls correctly. Moreover, with extended complier, our method creates source code randomization during its compiling and implements binary executable files randomization by feature matching. Our experiments on built prototype show that our method can effectively counter variety code injection attacks with low-overhead.