Method, apparatus and communication system for resource release controlling are provided in the disclosure. When a user equipment (UE) with an idle mode signaling reduction (ISR) being activated moves from a first source network to a second target network, if a first SGSN in the first source network knows that a second SGSN in the second target network does not support interaction with a serving gateway (S-GW) and does not support ISR, the first SGSN controls the deletion of bearer resources on a MME in the first network by sending a resource deletion message.