Provided is a secure apparatus for protecting the integrity of a software system and a method thereof. The apparatus comprises: a template repository for storing templates required for generating an agent module; a template generator for randomly selecting one template from said template repository and generating a new agent module according to the selected template; and a transceiver for sending said new agent module to an external apparatus communicating with said secure apparatus to update a current agent module which is running in said external apparatus, wherein said current agent module is used to verify the integrity of said software system running in said external apparatus. The secure apparatus can protect software in an insecure environment with a high software protection level to prevent the software from being tampered or bypassed.