This paper presents a compensation method of matrix converter drive system in case of commutation voltage error and unbalanced input voltage with disturbance observer. There are two compensation disturbances. One is commutation voltage error. This is caused by the dead-time between the turn-on and turn-off of the IGBT mode switches. The other is unbalanced input voltage. As the matrix converter has no DC-link, unbalanced input voltage cause the low performance to the output load. To realize high performance AC motor drive system, we can't ignore these problems. Adapting the disturbance observer by a feed-back proposed method to output current control, the robust control under these conditions can be realized. In this paper, the proposed method has been validated by the theoretical analysis with a Bode diagram and simulation results.