In this paper, a second-order-disturbance-observer-based distributed consensus control scheme is designed for a class of nonlinear multi-agent systems with input constraints. The second-order disturbance observer tracks the disturbance better than the common first-order disturbance observer. This paper provides the analysis of two kinds of disturbance observers and then compares the results from a simulation of the two types of observers. In the controller design process, a hyperbolic tangent function is used to limit output feedback in the control law. The overall closed-loop system reaches global stability with disturbance and the tracking errors exponentially converge without disturbance. The effectiveness of the proposed control law is illustrated by simulation results.