Inspired by aquaphotomics, the optical path length of measurement was regarded as a perturbation factor. Near-infrared (NIR) spectroscopy with multi-measurement modals was applied to the discriminant analysis of three categories of drinking water. Moving window-k nearest neighbor (MW-kNN) and Norris derivative filter were used for modeling and optimization. Drawing on the idea of game theory, the strategy for two-category priority compensation and three-model voting with multi-modal fusion was proposed. Moving window correlation coefficient (MWCC), inter-category and intra-category MWCC spectra, and k-shortest distances plotting with MW-kNN were proposed to evaluate weak differences between two spectral populations. For three measurement modals (1 mm, 4 mm, and 10 mm), the optimal MW-kNN models, and two-category priority compensation models were determined. The joint models for three compensation models’ voting were established. Comprehensive discrimination effects of joint models were better than their sub-models; multi-modal fusion was better than single-modal fusion. The best joint model was the dual-modal fusion of compensation models of one- and two-category priority (1 mm), one- and three-category priority (10 mm), and two- and three-category priority (1 mm), validation’s total recognition accuracy rate reached 95.5%. It fused long-wave models (1 mm, containing 1450 nm) and short-wave models (10 mm, containing 974 nm). The results showed that compensation models’ voting and multi-modal fusion can effectively improve the performance of NIR spectral pattern recognition.

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