An apparatus for generating heterogeneous functional equivalent and method thereof includes: a heterogeneous functional equivalent generator and an element pool connected to the heterogeneous functional equivalent generator, where the element pool includes at least one element. The heterogeneous functional equivalent generator is configured to obtain a generation policy and is further configured to select element sets corresponding to the number from the element pool according to the generation policy. The heterogeneous functional equivalent generator is further configured to generate the number of heterogeneous functional equivalents based on the selected element sets. Because the elements for constructing heterogeneous functional equivalents are different, the relationship between element and service response output by the heterogeneous functional equivalent to outside is uncertain, thereby making it uneasy to sniff an unknown defect or a backdoor of the heterogeneous functional equivalent, and lowering the success rate of an intruder's attack on the heterogeneous functional equivalent.