The house fly, Musca domestica L. is an important mechanical vector of different pathogens of medical and veterinary importance. It is an organism well-known for its ability to develop insecticide resistance. In the current study, we investigated the genetic basis and mechanism of chlorantraniliprole resistance in a field strain of house fly by selecting it artificially in the laboratory with a commercial formulation of chlorantraniliprole (CTPR-SEL). After seven generations of consecutive selection with chlorantraniliprole, CTPR-SEL strain developed a 644-fold resistance compared with the Susceptible strain and a 3-fold resistance compared with the field strain. Reciprocal crossing between the CTPR-SEL and Susceptible homozygous strains revealed an autosomal and incomplete dominant mode of resistance to chlorantraniliprole. A direct test using a monogenic inheritance model based on chi-square analysis revealed that the resistance was governed by more than one gene. Bioassays with synergists indicated that esterases might be involved in the resistance of house fly to chlorantraniliprole. These findings may be helpful to the development of an improved strategy for chlorantraniliprole resistance management in house fly.