Functional near-infrared spectroscopy (fNIRS) classification of mental states is of important significance in many neuroscience and clinical applications. Existing classification algorithms use all signal-collected brain regions as a whole, and brain sub-region contributions have not been well investigated. This paper proposes a functional region decomposition (FRD) method to incorporate brain sub-region contributions and enhance fNIRS classification of mental states. Specifically, the method iteratively decomposes the brain region into multiple sub-regions to maximize their contributions with respect to the validation accuracy and coverage of brain sub-regions. Then for the fNIRS data in brain sub-regions, features are extracted and classified to output the predictions. The final predictions are determined by fusing predictions from multiple brain sub-regions with stacking. Experiments on a publicly available fNIRS dataset showed that the proposed functional region decomposition method led to 9.01% and 10.58% increase of classification accuracy for the methods related to slope-based features and mean concentration change features, respectively. Therefore, the proposed method can decompose the brain region into sub-regions with respect to their functional contributions and fundamentally enhance the performance of mental state classification.