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In this paper, we establish and study a novel predator–prey model that incorporates: (i) the migration of prey between breeding and non-breeding regions; (ii) the refuge effect of prey; and (iii) the reduction in prey pulse birth rate, in the form of a fear effect, in the presence of predators. Applying the Floquet theory and the comparison theorem of impulsive differential equations, we obtain the sufficient conditions for the stability of the prey-extinction periodic solution and the permanence of the system. Furthermore, we also study the case where the prey population does not migrate. Sufficient conditions for the stability of the prey-extinction periodic solution and the permanence are also established, and the threshold for extinction and permanence of the prey population is obtained. Finally, some numerical simulations are provided to verify the theoretical results. These results provide a theoretical foundation for the conservation of biodiversity.