In this study, an adaptive hierarchical interval type-2 fuzzy control (AHIT2FC) scheme is presented for three-dimensional (3D) trajectory tracking control of an underactuated autonomous underwater vehicle (AUV), which has only three independent control inputs and is subject to partially parametric uncertainty and unknown external disturbances. To decrease reliance on hydrodynamic parameters, an interval type-2 fuzzy logic system (IT2FLS) is utilized, which exhibits superior capabilities in handling high levels of uncertainties prevalent in the underwater environment as compared to a type-1 fuzzy logic system. However, the traditional fuzzy system structure encounters the “curse of dimensionality” issue, which results in high computational complexity and imposes a significant burden on the limited computing resources underwater. The proposed AHIT2FC framework, based on a hierarchical structure, can substantially enhance computational speed while ensuring excellent control performance. Subsequently, Lyapunov’s theory is adopted to guarantee that all the tracking errors in the closed-loop system are semiglobally uniformly bounded (SGUB). Finally, comparative simulation results demonstrate the effectiveness and superiority of the proposed AHIT2FC scheme.