A computer system, a control method thereof and a recording medium storing a computer program thereof are provided to recover a program efficiently and be resistant to viruses, worms, and user error. The control method of computer system receives a user's request for a recovery of a program which is installed in a first storage unit. A file system of a second storage unit is determined which stores therein a recovery program corresponding to the program for which the recovery is requested. The recovery program is read from the second storage unit with reference to the determined file system, and the program in the first storage unit is recovered by using the read recovery program.