The Nb4AlC3 MAX phase can be regarded as a TMC structure with stacking faults, which has great potential as a novel solid hydrogen storage material. Herein, we used ab initio calculations for understanding the hydrogen incorporation into Nb4AlC3 MAX phases, including equilibrium structural characteristics, energy changes, electronic structures, bonding characteristics, and diffusion paths. According to the calculated results, H has thermal stability in the interstice of the Nb-Al layer, and the most probable insertion site is an octahedron (3-site) composed of three Nb atoms and three Al atoms. When C vacancies are introduced, the Nb-C layer has a specific storage capacity for H. In addition, Al vacancies can also be used as possible sites for H incorporation. Moreover, the introduction of vacancies significantly increase the hydrogen storage capacity of the MAX phase. According to the electronic structure and bonding characteristics, the excellent hydrogen storage ability of the Nb4AlC3 structure may be due to the formation of ionic bonds between H and Nb/Al. It is worth noting that the H-Al bond in the 1-site is a covalent bond and an ionic bond key mixture. The linear synchronous transit optimization study shows that only H diffusion in Al vacancies is not feasible. In conclusion, the Nb-Al layer in Nb4AlC3 can provide favorable conditions for the continuous insertion and subsequent extraction of H, while the vacancy structure is more suitable for H storage. Our work provides solid theoretical results for understanding the hydrogen incorporation into Nb4AlC3 MAX phases that can be helpful for the design of advanced hydrogen storage materials.