A method and apparatus for performing firmware programming on a microcontroller chip and the associated microcontroller chip are provided. The method includes: utilizing an integrated circuit (IC) programmer to generate a seed file including characteristic information of the IC programmer; utilizing an encoder to encrypt original data representing a program code at least according to the characteristic information, to generate an encryption version of the original data; utilizing the IC programmer to decrypt the encryption version of the original data according to the characteristic information, to generate the original data utilizing the IC programmer to encrypt the original data at least according to predetermined information, to generate another encryption version of the original data; utilizing the microcontroller chip to decrypt the other encryption version at least according to predetermined information stored in the microcontroller chip to generate the original data, and write the original data into a non-volatile (NV) memory.