An automatic thermal throttling protection method is described. a computer system executes a main BIOS for initializing an embedded controller when the computer system is power on or boots. And the sub BIOS of the embedded controller is also executed. The sub BIOS of the embedded controller obtains an upper temperature limit and a lower temperature limit set by the main BIOS, and obtains a temperature of the CPU through a thermal sensor. The sub BIOS of the embedded controller compares the temperature of the CPU with the upper temperature limit. When the temperature of the CPU is higher than the upper temperature limit, the sub BIOS sends a system control interrupt event to the main BIOS through the embedded controller. When receiving the SCI event, the main BIOS enables a throttling function to perform a throttling operation on the CPU or shuts down the computer system.