In this paper we established a predator-prey model with multiple refuges for prey. Based on two different time scales,applying the singular perturbation techniques we analyse the dynamics on the slow system. The stability analyses are performed and Hopf bifurcation occurs when the threshold condition is greater than one value. It is shown that adding refuges for prey may lead to stability lost. Furthermore,the case of one refuge and multiple refuges are compared. It is found that the migration of prey among patches affects the dynamics of predator-prey system. The effect of the migration between open habitat and refuges is stronger than that of the migration among refuges for prey.The refuge size also infects the dynamics of predator-prey system.