A service linkage control system and method are disclosed for implementing service linkage identification and control for separated control channel and data channel in the communication system. The method includes that: a linkage strategy management module (102) sends a first service template of the service needing linkage identification to a Deep Packet Inspection (DPI) identification module (101) to identify the service needing linkage identification, and sends after classification a service identification result and linkage related information to a linkage strategy management module (102) via a DPI identification device information collection database (104) and a linkage information control center (105); the linkage strategy management module (102) generates a service control strategy according to the received service identification result and a predetermined control rule, and issues the control strategy to a DPI control module (103); and the DPI control module (103) receives and implements the control strategy.