This article proposes a novel fractional-order sliding mode control based on the disturbance observer for a class of noncommensurate fractional-order systems with mismatched disturbances. Firstly, the noncommensurate fractional-order system is decomposed into several subsystems with commensurate order. Then the fractional-order disturbance observers are designed independently to estimate the mismatched disturbances for each subsystems. Based on the designed disturbance observers, a uniform fractional-order sliding mode control is proposed. The proposed method can deal with the mismatched disturbances and has better control performance. The simulations on single-link flexible manipulator system demonstrate the effectiveness of the proposed method.