Inconel 718 (IN 718) superalloys are widely used as engineering materials owing to their superior mechanical performance. And voids are unavoidable defects in IN 718 superalloy preparation, which dramatically affect the mechanical properties of IN 718 superalloys. In this work, the effects of void radius, distance from the top of the void to the substrate surface, and substrate temperature on the mechanical properties of the Ni/Ni3Al crystal are systematically investigated. It is shown that voids affect the formation of stair-rod dislocations and Shockley dislocations in the substrate, which in turn determines the mechanical properties. Thus, with the increase in void radius, Young’s modulus and hardness gradually decrease. With the increase in void distance, Young’s modulus and hardness increase and finally tend to be stable. In addition, the increase in substrate temperature leads to the interphase boundary becoming irregular and increases the defects in the γ and γ″ phases. As a result, Young’s modulus and hardness of the substrate decrease. This work aims to provide a guideline for investigating the indentation properties of Ni-based superalloys using MD.