A system for executing a program using a virtual machine monitor and a method of controlling the system are provided. The system includes a virtual machine monitor which divides an operating system (OS) into at least one root domain and a plurality of domains having different trust levels, and a trust-management module which is included in the root domain and periodically measures the trust level of an application program currently being executed in the OS. The virtual machine monitor executes the application program in one of the domains in consideration of the trust level of the application program. The method includes dividing an OS into at least a root domain and a plurality of domains having different trust levels by using a virtual machine monitor, enabling the root domain to periodically measure the trust level of an application program currently being executed in the OS, and executing the application program in one of the domains according to the trust level of the application program.