To realistically reflect the shear performance of the rock-filled concrete (RFC) between layers, this study relies on an RFC dam project in Guizhou Province. Test blocks, measuring 5 m × 4 m × 2 m with cold joints, were cast on site and subjected to shear tests. Additionally, a three-dimensional four-phase meso-model was developed, considering the mutual contact effects between component materials. The mechanical response and damage mechanism of the interlayer were analyzed using the cohesive zone model. The results confirm that the cohesive zone model effectively simulates interlayer cold joint structures. The damage modes of the RFC interlayer include cold joint debonding damage (Mode I) and plastic extrusion damage of self-compacting concrete (Mode II). As the exposed height of the rocks increases, the damage mode shifts from Mode I to Mode II, and higher normal stresses intensify Mode II damage. Meanwhile, the paths of crack extension depend on the distribution of shear-resistant rocks, with weak interfacial transition zones serving as “bridges’’ for crack propagation. The interlayer shear strength is positively correlated with the average exposed height of rocks and normal stresses, with the former having a more significant impact. Finally, the accuracy of the proposed shear strength prediction model for the RFC interlayer was validated by comparing it with results from other studies, providing useful references for meso-numerical modeling of RFC.