A handover apparatus and method in a communication system having a macro BS and a plurality of micro BSs in one cell are provided. A handover apparatus includes a macro BS for generating a plurality of messages, each messages respectively corresponds to one of a plurality of group areas defined by grouping service areas of the micro BSs and includes information about BSs to which MSs of the group area can perform handover. The macro BS also generates group area information indicating locations of the group areas, broadcasts the plurality of messages and the group area information to the cell, and manages handover of MSs based on the plurality of messages and the group area information.