Paris polyphylla var. yunnanensis is a famous medicinal plant distributed in some Asian countries. This species has attracted a great deal of attention and is often used as raw materials in traditional medicine practices. With the purpose of gaining insight into the geoherbalism of wild P. polyphylla var. yunnanensis, a total of 183 dried rhizome samples from eight different regions including 16 typical or nontypical natural habitats have been analyzed by multispectral information fusion based on ultraviolet and Fourier transform infrared spectroscopies combined with partial least squares discriminant analysis (PLS-DA) and hierarchical cluster analysis. From the results, the use of multispectral information fusion strategy could improve the correct classification of samples, and good classification performances have been shown according to PLS-DA models. The discrimination of samples was obtained successfully with respect to the typical and nontypical natural habitats, different collection areas of typical natural habitats, and various sampling sites in nontypical natural habitats. Additionally, the similarities among samples were presented as well. Overall, the rhizome of wild P. polyphylla var. yunnanensis exhibited various regional dependence and individual differences according to the geographical origins, and the relatively appropriate growth region with better quality consistency of samples was preliminarily selected. This study also revealed that the developed multispectral information fusion method has the potential to be a reliable analytical methodology for capturing the geoherbalism differentiation in wild P. polyphylla var. yunnanensis. Furthermore, it could provide more chemical evidence for the critical supplement of quality evaluation on P. polyphylla var. yunnanensis.