We investigate theoretically the formation mechanisms of the unintentional compositional gradient layer occurring at AlGaN/AlN heterointerfaces during metal–organic chemical vapor deposition (MOCVD). The study of heterointerface morphology is crucial for developing AlGaN deep-ultraviolet light-emitting laser diodes. After studying the stability of the surface reconstructions with intrinsic point defects in their subsurface layers using an ab initio-based approach, we inspect the impact of defects on the atomic interdiffusion at the heterointerfaces by Monte Carlo simulation. The relationship between MOCVD conditions and the type of dominant intrinsic point defects is clarified. We find that (i) cation and anion vacancy complexes are dominant in the subsurface layers above 1000 °C and (ii) they accumulate near the AlGaN/AlN heterointerface during growth, causing cation interdiffusion, i.e., the formation of compositional gradient layers. Controlling the type of intrinsic point defects incorporated during the surface growth in MOCVD is a key factor in preserving atomically flat heterointerfaces.