One of the important factors affecting the anchoring force of the end encapsulated bolt is the mechanical properties of the rock formation at the anchoring end. For the fully encapsulated bolt, its bearing performance is closely related to the mechanical properties of the bolt passing through the rock stratum and its permutation mode. In this study, a series of laboratory pull-out tests of multi-strata anchorage systems was carried out based on an actual engineering background. The bearing performances and failure mechanisms of the multi-strata anchorage system under different anchoring methods and combinations of rock stratum were studied. The evolution law of the axial force and shear stress of the Agent-Rock interface was also analyzed. The test results showed that, for end encapsulation, changes in the mechanical properties of the rock strata at the anchoring end caused differences in bearing capacity, while full-length encapsulation markedly reduced the disparities. The position of the stratum with the highest general interface shear strength affected the mechanical response of the anchoring interface. The progressive failure process of multi-strata anchorage systems was discussed, and suggestions for rock bolt support in coal mine roadways were also proposed.