In recent decades, species extinction has become one of the most important issues in ecology and conservation biology. Such extinctions are mainly caused by habitat destruction. The destruction has no possibility of recovery for endangered species unless the destroyed habitat is restored. Furthermore, even if the destruction is restricted to a local area, its accumulation increases the risk of extinction. Habitat destruction not only reduces the habitat area but also fragments the habitat. In the present article, we introduce three types of destruction models. i) Bond destruction: the fragmentation occurs, but habitat area is never reduced. ii) Random site destruction: both fragmentation and area loss occur. iii) Rectangular site destruction: the habitat area is reduced, but fragmentation never occurs. We apply a lattice system composed of prey and predator, and compare the effects of the three types of habitat destructions. Simulations reveal that outcomes entirely differ for the different models. The density of prey or predator undergo complicated changes by destructions. The habitat fragmentation is much more serious for species extinction than the area loss of habitat. In our simulation, extinction only occurs for fragmentation models. For the random site destruction, we universally obtain a "40% criterion": when the proportion of destroyed sites exceed percolation transition (40%), the risk of species extinction suddenly increases. Moreover, we find an asymmetric effects on predator and prey. In all destruction models, the steady-state density of predator tends to decrease with the increase of the magnitude (D) of the destruction. In contrast, the effect on prey is rather opposite: prey density usually increases with increasing D.