Human-caused habitat destruction is one of the greatest threats to species diversity. In spatially implicit model, habitat destruction is just a single parameter, a reduction of the fraction of available sites, while in spatially explicitly model, habitat fragmentation has been taken into consideration. Therefore, contrast to spatially implicit model, spatially explicit model is more close to reality. Cellular automation is one of the most widely used（popular） spatially explicit models. Cellular automata models provide realistic, effective and reliable models of the spatiotemporal dynamics of metapopulation. Therefore, in this article cellular automation model was constructed to simulate the responses of species diversity to human-caused habitat destruction at ten-thousand year time scale, millenary time scale and century time scale, respectively. The results show that: The bigger q is, the longer the species extinction time is. So, the characteristics of species response to habitat destruction are deeply influenced by the metapopulation structures. Species go extinct in ranked competitive order (i.e., species 1 followed by 2, by 3 ) at ten thousand time scale, while at millenary time scale, the order of species extinction will greatly depend on the structure of metapopulation. When q (the proportion of occupied patches by best competitors) is bigger, species will go extinct from the best to the worst before complete destruction, and the survivals will go extinct collectively when complete destruction; when q is smaller, because the differences of species abundance and dispersal abilities among different species are not significant, the order of species extinction is not deterministic, and it is possible for the best competitor go extinct finally. While at century time scale, species will go extinct collectively at the moment of complete habitat destruction because the habitat destruction is so intensive and quick that species have no time to response. Therefore, the order of species extinction is influenced not only by the dispersal abilities, but also by the different speeds of habitat destruction and the structure of metapopulation. Therefore, to preserve different species, we should exploit different habitat at different rates.