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In the study, an aqueous two phase system (ATPS) coupled with ultrasound was employed to extract lignans from Zanthoxylum armatum. Three standard lignans, namely (−)-fargesin, sesamin and L-asarinin, were used as marker compounds, and extraction was optimized and projected by response surface methodology (RSM) and artificial neural network (ANN). The optimal condition for ATPS with 20% n-propanol and 24% (NH4)2SO4 coupled with ultrasonic-assisted extraction including a solvent to solid ratio of 15:1, a temperature of 40 °C, and a treatment time of 55 min was obtained. Under the condition, the yield of (−)-fargesin increased 15.12%, and the purities of (−)-fargesin, sesamin and L-asarinin reached 2.222%, 1.066%, and 1.583%, with an increase of 44.38%, 25.70%, and 26.34% compared to those extracted with 95% ethanol, respectively. Coefficient of the determined (0.9855) and mean squared error (0.0018) of ANN model suggested good fitness and generalization of the ANN. Taken together, the results showed that ultrasonic-assisted ATPS can be a suitable method for extraction and enrichment of lignans from Z. armatum.