Web servers are widely deployed on cloud computing platform represented by Docker containers and face serious security challenges. In order to improve the security and defense capability of such Web servers, a dynamic defense method of Web server based on Linux namespace was proposed. Firstly, the running environment of Web server was built by using namespace on the premise to ensure Web service working normally. Then, the dynamic transformation of Web server was realized by the alternate running of multiple environments to confuse intruder, which increased the difficulty of attacking Web server by the intruder. Finally, the running environment of Web server was periodically deleted and rebuilt to eliminate the impact of intrusion behavior on the Web server, and ultimately the dynamic defense capability of Web server was effectively improved. The experimental results show that, the proposed method can effectively enhance the security of Web server while it has little affect on system performance, and its response time of requesting 100 KB data is 0.02-0.07 ms.