A system and method for managing resources in a heterogeneous network, which includes a primary system and a secondary system, and in which a communication coverage range of the primary system is divided into a plurality of regions, the system including: a heterogeneous network resource management module configured to collect and manage resource usage status within a managed region; and a secondary system resource management module configured to acquire the resource usage status of each region from the heterogeneous network resource management module and to allocate resources to the secondary system by utilizing the acquired resource usage status of each region in accordance with a priority determined based on an efficiency of resource multiplexing between the primary system and the secondary system in each region. The system and method improve resource usage efficiency.