Controlling invasive alien species invasion and maintaining the survival of native species have attracted increasing attention, and habitat destruction can be used to achieve these aims. However, it remains unclear whether and how to promote the long-term survival of indigenous species facing invaders through the use of habitat destruction. In this study, we developed a spatially explicit simulation model and exposed invaders and residents from this model to habitat destruction with different properties. The results showed that (1) introducing habitat destruction could promote the long-term survival of native species facing invaders; however, the promoting effect of habitat destruction occurred only over a period of time after introduction, and habitat destruction substantially weakened indigenous species before that. (2) Intermediate levels of habitat destruction were the most beneficial to the protection of native species. (3) Even if not considering the proportion of destroyed habitats, introducing spatially dispersed habitat destruction at an earlier time and shortening the interval between two habitat destruction events were very beneficial to the protection of residents. These insights can help facilitate the protection of residents under invasion by adjusting the implementation method of habitat destruction.