Selective catalytic reduction of NO with methane (NO-CH4-SCR) in the presence of excess oxygen was investigated over the synthesized MnH-ZZs-n zeolite composite catalysts with FAU (as core) and BEA (as shell) topologies. XRD, SEM, and NH3-TPD technologies were employed to characterize the catalysts. It is found that the topological structure of the zeolite affected the catalytic properties and H2O/SO2 tolerances considerably. MnH-ZZs-n catalysts exhibited much higher NO-CH4-SCR activity than the physical mixture catalysts with comparable relative mass content of Y and Beta zeolites, particularly the ratio of Y and Beta at the range of 0.2–0.5 than the MnH-Beta catalysts with single topology. NH3-TPD results showed that one new type of strong acidic sites formed in H-ZZs-n and remained in MnH-ZZs-n resulted from the interaction between the Lewis and Brönsted acid sites under a particular environment. The special zeolite-zeolite structure with ion-exchanged Mn ions in the core-shell zeolite composite catalysts contributed to the novel NO-CH4-SCR properties.