The invention discloses an encryption method and running method of a JAVA application. The encryption method includes the steps that firstly, the integrity of an executable file of a JAVA virtual machine and a class loading basis device is examined; secondly, the safety of communication between an execution file examiner and the class loading basis device is guaranteed by checking a random character string; thirdly, a first secret key is written into computer program input stream of the class loading basis device; finally, after the class loading basis device obtains the first secret key from the computer program input stream, in cooperation with a randomly-generated second secret key for user holding, a decoding file of the JAVA application is encrypted, and the encrypted decoding file and the second secret key are output. The running method similarly includes the steps that firstly, the integrity of the modules is examined; secondly, the safety of communication is guaranteed; finally, the JAVA application is loaded and decrypted through the obtained first secret key and the user-input second secret key. According to the encryption method and running method, both the safety of the JAVA application and the high transportability and compatibility of the JAVA application are guaranteed.