An apparatus and a method for detecting interference in a heterogeneous system of a mobile communication system that uses an Industrial, Scientific and Medical (ISM) band are provided. More particularly, an apparatus and a method for determining a start section and an end section of a packet using an Automatic Gain Control (AGC) change in a Zigbee communication system that uses an ISM band and detecting interference in a heterogeneous system using a reception rate of a packet and an interference occurrence rate depending on whether a synchronization process is performed during the determined section. The apparatus includes an interference detector. The interference detector determines a reception section of a packet by determining a start and an end of the received packet, determines whether a packet is synchronized during the determined section, and determines interference occurrence and a packet reception rate depending on whether the packet is synchronized.