The invention discloses a differential detection control plane fault diagnosis system and an implementation method thereof. The system comprises a data acquisition module, an online monitoring module,an offline fault diagnosis module and a network event replay engine. The implementation method comprises steps of acquiring code calling and state change information in the controller through the online monitoring module and the data acquisition module, and constructing a context-aware system behavior model; when the current system is not abnormal, extracting a system behavior model and storing the system behavior model in a reference library as a reference model; when the system finds out abnormity, finding out a system behavior model with a fault and a corresponding reference model according to the symptom of the fault; Difference comparison is carried out on the nodes from top to bottom, and abnormal nodes are found out; And then, carrying out static analysis at the abnormal nodes, finding out the source of the fault at the code level, confirming the source through a network event replay engine in a simulation environment, and submitting the source to an administrator as a fault diagnosis report. The fault source can be positioned, and the applicability is high.