Habitat destruction is the primary cause of extinction. There are two broad categories of the heterogeneity of habitat destruction: spatial and temporal heterogeneities. Previous studies mostly focus on one category and do not integrate one with the other. Therefore, we integrate the spatial heterogeneity with the temporal heterogeneity into cellular automata to study the response of metapopulation dynamics to the temporal-spatial heterogeneity of habitat destruction. The results show that: under random and discrete habitat destruction, superior competitors, but poorer colonizers, will go extinct first because their colonization abilities are deeply affected by habitat destruction. Under continuous destruction, however, colonization abilities are affected slightly by habitat destruction, and species extinction is determined by competition abilities and colonization abilities together. In the community with absolute dominance species and good colonization ability, inferior competitors will go extinct first due to strong specific-competition. While in the community without dominant species and with poor colonization ability, superior competitors will go extinct first due to poor specific-competition. Therefore, random destruction is not favorable to the persistence of superior competitors, while continuous destruction is not favorable to the persistence of inferior competitors in the community with good colonization ability. So, when exploiting a certain habitat, we should take different action according to different conservation objects and metapopulation with different structures.