A computer system with integrated storage device for storing both a basic input/output system (BIOS) code and an operating system (OS) code and an associated booting method are provided. The computer system includes a central processing unit, a storage device controller and the storage device. The BIOS code and the OS code are stored in an invisible are and a visible area of the storage device, respectively. At first, the storage device controller is activated to read data from an architecture information area of the storage device to perform initialization. Then, the initialized storage device controller converts a read-only memory access command issued from the central processing unit into a suitable format to control loading of the BIOS code from the invisible area. At last, the storage device controller controls loading of the OS code from the visible area to finish the booting of the computer system.