We prove that a certain eventually homological isomorphism between module categories induces triangle equivalences between their singularity categories, Gorenstein defect categories and stable categories of Gorenstein projective modules. Furthermore, we show that the Auslander-Reiten conjecture and the Gorenstein symmetry conjecture can be reduced by eventually homological isomorphisms. Applying these results to arrow removal and vertex removal, we describe the Gorenstein projective modules over some non-monomial algebras and verify the Auslander-Reiten conjecture for certain algebras.