The invention discloses a deep code obfuscation method for Android system applications. The method uses graded code obfuscation. The graded code obfuscation includes first-grade name replacement obfuscation, second-grade command insertion obfuscation, third-grade structure process obfuscation, and fourth-grade command inversion obfuscation. For an application installation package developed and to be released, the method includes: extracting a DEX file, analyzing the file structure, a Dalvik instruction set and a program running process, determining an obfuscation scheme of corresponding grade or multiple combined grades to perform deep code obfuscation on the DEX file, generating a new DEX file, and re-packaging the file. The deep code obfuscation method according to the technical scheme has the advantages that the limitations of the traditional source-code-based code obfuscation scheme can be broken through, the DEX executable files are directly obfuscated in terms of element name, instruction and process structure, applications can be effectively protected from illegal cracking or inversion, safety of applications in the Android system is improved, and confidentiality of business software is guaranteed.