Abstract: The application of the Mamdani, TakagiSugeno fuzzy neural network, and BP neural network in clinical pathway control was investigated. The analyzing method for clinical pathway variations based on fuzzy neural network with knowledge was given. Finally, a case study on liver poisoning of osteosarcoma preoperative chemotherapy was used to validate the proposed method, and their effectiveness, and respective advantages and disadvantages were analyzed. The result shows that knowledge fuzzy neural networks have obvious advantages over standard neural networks for analyzing and reasoning of clinical pathway variations.