As the recent deployment of Cloud Computing like AmazonEC2, the price of hosting services is falling rapidly. Therefore, we had developed the Web based hosting system to handle huge number of hosts (about 2,000 hosts by a server) using Apache VirtualHost that single process manages multiple hosts and distinguish contents by the hostname with the access for minimizing the use of resources. However, it was difficult to manage the Web based hosting system, and the problems of the system were improvement of operation technology and designing the security mechanism with little performance degradation. In this paper, we clarify the problems of security and operation technology with installing VirtualHost for building a large-scale system, and we propose the approach solving them by developing the new Apache modules and enhancing suEXEC. This approach is help to building a large-scale, reliable and operationally-effective Web based hosting system.