The speeds of species extinction reach the climax in history and earth is facing the greatest mass extinction during the past 6500 millions. In the meanwhile, Habitat destruction is the most pervasive and pernicious human impact on other species and the major cause of biodiversity loss. Therefore, there are many studies on the effects of habitat destruction on species diversity through spatial implicitly models or spatial explicitly ones. Because the pattern of habitat destruction in real landscape is random, it can not be ignored. Spatial explicitly models, especially for cellular automata, are widely used because of their consideration of spatial patterns. However, few studies have studied the dynamics of population spatial patterns in fragmented habitat through fractal geometry. So, we have studied the dynamics of the population spatial patterns in fragmented habitat and metapopulation dynamics response to the spatial heterogeneity of habitat destruction through the integration of cellular automata and fractal geometry at the first time. The results show that: （1) the spatial distribution patterns of population have fractal characteristics. Box dimension can represent not only population spatial patterns, but also population dynamics. （2) By taking spatial factors into consideration, the extinction debt will be much greater.（3) There is the extinction not only of superior competitors, but also of inferior ones. Only under random destruction, will the results (i.e., the best competitor will go extinct at first.) be similar to those under spatial implicitly models. It will be the third best competitor that goes extinct first. （4) Aggregated destruction such as edge destruction is more favorable to species persistence than random destruction, especially for inferior competitors.