A method of updating firmware in a chip in a stable and effective manner receives firmware outputted by a controller. The received firmware is burned into the chip. A voltage level of a controlling signal outputted by a controlling pin of the chip is latched to a certain level based on a latching signal at a first voltage level outputted by the controller. The storage medium is refreshed for making the burned firmware effective based on refresh instruction outputted by the controller. The latching signal at a second voltage level for unlatching the voltage level of the controlling signal is outputted by the controller if operations of the chip are stable. An updating operation of the chip by the method does not interrupt other operations being executed by the chip. A firmware updating apparatus and a computer readable storage medium applying the method are also disclosed.