To solve the problem of low efficiency in digital generating machining for producing small or medium batches of helical gears, a method to improve the machining efficiency with an indexable disk milling cutter is presented in this paper. First, the mathematical model of the tooth profile and the indexable disk milling cutter are established. Second, according to the spatial free-form envelope theory, the overall planning scheme of the tool path is given; the relative position and the relative transformation matrix of the tool and tooth profile during digital generating machining using the indexable disk milling cutter are solved, the simulation cutting and actual cutting experiments are conducted, and the cutting efficiency per unit time and cutting simulation time of the two tools under the same deformation conditions is obtained through a finite element analysis experiment. The results show that the cutting efficiency of the indexable disk milling tool was 2–3 times higher than that of the end mill cutter.