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Agroforestry system, as the most promising substitute plantation approach, has been widely regarded as a prominent strategy for mitigating the conflicts between rapid growing population and limited arable land resources. This paper aims to screen the optimal planting pattern for <i>Gentiana rigescens</i> base on the content of gentiopicroside, providing the scientific basis for sustainable supply and application of this plant. Generally, Fourier transform infrared (FTIR) spectroscopy is effective to integrally monitor and reflect the whole constituents of natural materials. FTIR combined with chemometrics was used for distinguishing the <i>G. rigescens</i> from different compound planting models in this research. The result of partial least square discriminant analysis implied that planting year of <i>G. rigescens</i> had a greater impact on the content of gentiopicroside than that of <i>Camellia sinensis</i>. The gentiopicroside content in 1.5- or 2-year-old <i>G. rigescens</i> was higher. Wavelet denoising was effective for the classification. Samples which had higher contents of gentiopicroside were clustered together relatively, while those with lower contents of gentiopicroside were classified into the other large category. Our investigation revealed that <i>G. rigescens</i> can be successfully cultivated with <i>C. sinensis</i>, which met the requirement of the gentiopicroside content recommended by Pharmacopoeia of the People’s Republic of China. That 2-year-old <i>G. rigescens</i> grown with 12-year-old <i>C. sinensis</i> was the optimal compound planting pattern, according this study. The present study provided the optimal compound planting pattern of <i>G. rigescens</i>, which is helpful for improving land-use efficiency and economic returns.