The present disclosure provides a system and method for automatically configuring multiple chassis links in a multi-chassis system using a management controller. The management controller can request and receive switch port data from a plurality of server systems, and a plurality of switches of the multi-chassis system. Based upon received switch port data, the management controller can determine peer link ports for a first switch and a second switch of the plurality of switches; select suitable port groups from a plurality of ports of the first switch and the second switch based upon the received switch port data; and configure ports in each suitable port group as a MC-LAG member port for the corresponding suitable port group.