We studied the flow characteristics of the polymer melt in the injection molding process with ultrasonic vibration by using the numerical analysis. To minimize the error between the experimental data and numerical result, we presented a methodology using the design of experiments and the response surface method for reverse engineering. This methodology can be applied to various fields to obtain a valid and accurate numerical analysis. Ultrasonic vibration is generally applied between an extruder and the entrance of a mold for improvement the flow rate in injection molding. In comparison with the general ultrasonic process, the mode shape of the mold must be also considered when the ultrasonic vibration is applied on the mold. The mode shape is defined as the periodic and spatial deformation of the structure owing to the effect of the vibration, and it varies greatly according to vibration conditions such as the forcing frequency. Therefore, we considered new index and found the forcing frequency for obtaining the highest flow rate within the range from 20 to 60 kHz on the basis of the index. Ultimately, we presented the methodology for not only obtaining a valid and accurate numerical analysis, but also for finding the forcing frequency to obtain the highest flow rate in injection molding using ultrasonic vibration.