In this study, with the help of a disturbance observer, an adaptive fractional-order sliding mode control scheme is designed to achieve trajectory tracking control of indeterminate manipulators. Firstly, the fractional-order non-singular fast terminal sliding mode (FO-NFTSM) surface is presented to increase the convergence velocity of the controller. Secondly, the adaptive reaching law is designed on the strength of the super-twisting algorithm to ensure the control performance of the approaching stage. Meanwhile, aiming at the compound disturbance existing in the manipulator system, an adaptive fixed-time sliding mode disturbance observer (AFSMDO) is introduced to settle the problem, which can estimate the lumped disturbance in real-time. Moreover, compensate for the system and raise the precision of the controller. The Lyapunov method is applied to certify the stability of the control system. Simulation experiments verify the superior property of the controller designed in this article.