A multi-mode operation system and method for computer systems is proposed. The system includes a storage device having first and second disk partitions, a mode controller and a master boot program. The master boot program checks the status of the mode controller. If the computer system is running in PC mode, the master boot program hides the second disk partition, boots from the first disk partition, and loads a complete version of an operating system therein, thereby enables the computer system to run in the PC mode. If the computer system is running in a sub-mode being defined as an entry of a multimedia mode class, such as a music playing mode or video playing mode, the master boot program activates the second disk partition, boots therefrom, and loads a refined version of the operating system therein, thereby enables the computer system to run in the selected sub-mode.