In this study, a novel pattern recognition method named boosting–partial least squares–discriminant analysis (Boosting-PLS-DA) was developed for the non-destructive and accurate origin identification of food and medicine homologous substances (FMHSs). Taking Gastrodia elata, Aurantii Fructus Immaturus, and Angelica dahurica as examples, spectra of FMHSs from different origins were obtained by portable near-infrared (NIR) spectroscopy without destroying the samples. The identification models were developed with Boosting-PLS-DA, compared with principal component analysis (PCA) and partial least squares–discriminant analysis (PLS-DA) models. The model performances were evaluated using the validation set and an external validation set obtained one month later. The results showed that the Boosting-PLS-DA method can obtain the best results. For the analysis of Aurantii Fructus Immaturus and Angelica dahurica, 100% accuracies of the validation sets and external validation sets were obtained using Boosting-PLS-DA models. For the analysis of Gastrodia elata, Boosting-PLS-DA models showed significant improvements in external validation set accuracies compared to PLS-DA, reducing the risk of overfitting. Boosting-PLS-DA method combines the high robustness of ensemble learning with the strong discriminative capability of discriminant analysis. The generalizability will be further validated with a sufficiently large external validation set and more types of FMHSs.