This article introduces a three-degree-of-freedom (3DOF) model-based adaptive fractional-order dynamic surface control (AFODSC) system for a synchronous position control of a gantry table. First, the 3DOF model of the gantry table is investigated considering the rotational dynamics caused by inter-axis mechanical coupling and synchronous error. Then, a new fractional-order dynamic surface control (FODSC) approach is introduced using a fractional-order low-pass filter to provide an extra degree of freedom for the existing dynamic surface control (DSC) method. Because it is arduous to know the system uncertainty, the AFODSC is further elaborated by incorporating an adaptive mechanism and an uncertainty observation into the FODSC. In the proposed AFODSC, a modified dendritic neuron model observer (DNMO) is proposed to identify uncertainties, whereas an exponential compensator is designed to compensate for the observation error. Multiple adaptation laws are derived to adapt the parameters of DNMO on the basis of the Lyapunov stability theorem. Experimental results confirm that the proposed AFODSC system demonstrates favorable position tracking and synchronization accuracies for the gantry table compared with the conventional DSC system.