With the rapid development of Internet in the world, E-commerce has become a new research field, and the digital copyright protection in E-commerce has also become a big concern of society. The conventional method of copyright protection is to search information of digital works with search engine, and download them to a server where all digital works would be authenticated. In this paper a new copyright protecting system based on mobile agent and trusted third party is proposed, which can authenticate the digital watermark of digital works directly in the remote mainframe by using the distribution and transfer character of mobile agent. Then the results of the authentication will be sent back to the server. Therefore the convenient disadvantage of server load overweight is solved, and the efficiency of copyright protecting and tracing is greatly improved.