Stomachache is not only disease name of Traditional Chinese medicine (TCM) but also the clinical symptom. It is a common and multiple diseases. TCM has its particular advantage in clinical treatment of stomachache. Syndrome differentiation is an important concept in TCM practice. The therapeutic process is virtually a nonlinear mapping process from clinical symptom to syndrome diagnosis with processing and seeking rules from mass data. Artificial neutral network has strong learning ability for nonlinear relationship. Artificial neutral network has been widely used to TCM area where the multiple factors, multilevel, nonlinear problem accompanied by a large number of optimization exist. We present an original experimental method to apply the improved third-order convergence LM algorithm to intelligent syndrome differentiation for the first time, and compare the predicted ability of Levenberg-Marquardt (LM) algorithm and the improved third-order convergence LM algorithm in syndrome differentiation. In this study, 2436 cases of stomachache electronic medical data from hospital information system, and then the real world data were normalized and standardized. Afterwards, LM algorithm and the improved third-order convergence LM algorithm were used to build the Back Propagation (BP) neural network model for intelligent syndrome differentiation of stomachache on Matlab, respectively. Finally, the differentiation performance of the 2 models was tested and analyzed. The testing results showed that the improved third-order convergence LM algorithm model has better average prediction and diagnosis accuracy, especially in predicting “liver-stomach disharmony” and “stomach yang deficiency”, is above 95%. By effectively using the self-learning and auto-update ability of the BP neural network, the intelligent syndrome differentiation model of TCM can fully approach the real side of syndrome differentiation, and shows excellent predicted ability of syndrome differentiation.