1. A method for comparing a first subroutine and a second subroutine in functionality, comprising: defining a plurality of instruction sets, each of which being associated with a corresponding instruction set process; performing a capturing process to obtain a first program section and a second program section respectively from the first subroutine and the second subroutine, and respectively categorizing the first program section and the second program section to one of the instruction sets; and performing a program section comparison process to select and perform one of the instruction set processes according to the instruction set to which the first program section is categorized and the instruction set to which the second program section is categorized, so as to compare whether the first program section and the second program section are identical in functionality.