The present invention provides a method and a system for generating a multi-factor authentication code. The method comprises steps of generating a plurality of random numbers that are completely random; arranging the plurality of random numbers into a combination in a time-series or a random way; dividing the combination into a plurality of sub-combinations; transmitting each of the plurality of sub-combinations to one of corresponding plurality of interfaces respectively via one path according to a distributing rule; combining the plurality of sub-combinations received by the plurality of interfaces to form the multi-factor authentication code according to a combining rule. And the system comprises a processor being programmed to function as: a random number generator, an arranging unit, a dividing unit, a transmitting unit, and a combining unit.