Abstract: The present disclosure discloses an information security application-oriented reconfigurable system chip compiler and an automatic compilation method. The method includes the following steps: firstly, inputting a source program of a cryptographic algorithm; then, executing a software compilation function syntax check of the source program, and when the check result is passed, performing compilation mapping using a compiler; next, executing the cryptographic algorithm by simulation running using a simulator, and generating a configuration code by a simulator array; and finally, guiding a hardware behavior operation using a binary configuration code file generated by the simulator. The reconfigurable system chip compiler includes a source program input module, a software compilation function verification module, a compilation mapping module, a simulation execution module, a configuration code generation module, and a hardware debugging module.