Biomechanical effect of posterior intra-articular cages and cantilever technique on the congenital basilar invagination (BI) combined with atlantoaxial dislocation (AAD) was investigated and evaluated using finite element (FE) analysis. A 3D nonlinear occipitocervical segment C0-C3 FE models of congenital BI and AAD was established. Then, the FE model treated with C2 pedicle screw and occipital plate fixation coupled with intra-articular cages (Cage + C2PS + OP) was compared to that without intra-articular cages (C2PS + OP). The range of motion (ROM) of C0C1-C2 and the maximum von Mises stresses (MVMS) on the intra-articular cages, screw-plate system, and C2 endplate were calculated and compared to further analyze the stability of atlantoaxial joint and assess the collapse and fracture risks of intra-articular cages and screw-plate system. ROM of C0C1-C2 segment was reduced by 57.58%, 63.33%, 78.18%, and 75.90%, and the peak stresses of C2 pedicle screw and occipital plate were decreased by 84.86%, 72.90%, 73.24%, and 84.90% and 78.35%, 76.64%, 81.82%, and 89.49% for Cage + C2PS + OP model in flexion, extension, lateral bending, and axial rotation when compared with the C2PS + OP model under the same condition. The MVMS of intra-articular cages were 13.80 MPa, 40.26 MPa, 26.93 MPa, and 17.50 MPa and those of C2 endplate were 14.56 MPa, 34.80 MPa, 36.29 MPa, and 37.56 MPa in Cage + C2PS + OP model under same conditions. Posterior intra-articular cages and cantilever technique to treat BI-AAD can improve the stability of the atlantoaxial joint and reduce the risk of screw-plate breakage. The intra-articular cages can not only complement the height loss on account of atlantooccipital fusion but also provide stable support for posterior fixation fusion.