Tracking control problem of the leader-follower multi-agent systems with unmatched uncertainties and input saturation is investigated. An auxiliary system and extended state observer is imported to approximate system position states. Unknown disturbances of system are estimated by a sliding-mode disturbance observer. A sliding mode disturbance observer based control protocol is proposed and the stability is guaranteed via Lyapunov theory analysis. In addition, the effect of unknown saturation input can be estimated and compensated by the sliding-mode disturbance observer. The feasibility of the theoretical analysis is validated through a numerical simulation.