Objective Various environmental factors make the chemical composition of cultivated Paris polyphylla var. yunnanensis also rich and diverse, and the steroidal saponins of Paris polyphylla var. yunnanensis in different origins are quite different. An efficient and accurate identification model of different origins is established to provide a basis for the rational development and utilization of its resources. Methods A total of 366 rhizomes from 8 origins in Yunnan and Sichuan provinces (Baoshan, Chuxiong, Dali, Honghe, Lijiang, Chengdu, Wenshan, Yuxi) were used as experimental materials, and their Fourier transform near-infrared spectra (FT-NIR) and attenuated total reflection-Fourier transform mid-infrared spectroscopy (ATR-FTMIR) data were collected. The Kennard-Stone algorithm was used to divide samples from different origins into 2/3 training set and 1/3 prediction set. Based on 4 feature variable extraction methods (CARS, VIP, SPA, SO-Covsel) combined with 2 data fusion strategies (Low-level data fusion and intermediate-level data fusion), the partial least squares origin discriminant analysis model was erected. According to the model parameters, cross-validation root mean square error (RMSECV) and prediction root mean square error (RMSEP) were used to evaluate the performance of the model, and the accuracy of training set and prediction set were used to evaluate the model classification performance. Results Both near-infrared and mid-infrared spectra could reflect the differences of cultivated Paris polyphylla var. yunnanensis in different origins. In the mid-level data fusion models, the accuracy of the models established based on the feature variables extracted by VIP and SPA were both greater than 94%. Compared with the mid-level data fusion models, the low-level data fusion model obtained the most satisfactory results, and its accuracy reached 100%. Conclusion The low-level data fusion PLS-DA model established based on the near-infrared and mid-infrared data can be used for the identification and analysis of the cultivated Paris polyphylla var. yunnanensis.