A method for automatically optimizing a configuration of a BIOS is suitable for configurating a computer system. During a BIOS power-on self test, a running operating system predetermined index is obtained from a memory. An optimal system setting parameter corresponding to the running operating system predetermined index is obtained. The computer system is automatically set up according to the optimal system setting parameter. A booting process is performed to start an operating system. An operating system index of the operating system is obtained. The operating system index is compared with the running operating system predetermined index. When the operating system index is not equal to the running operating system predetermined index, a system setting warning is issued. The running operating system predetermined index is updated by using the operating system index as the updated running operating system predetermined index in the memory.