Maize is susceptible to mold infection during growth and storage due to its large embryo and high moisture content. Therefore, it is essential to distinguish the moldy sample from healthy groups to prevent the spread of mold and avoid huger economic losses. Catalase is a metabolite in the growth of microorganisms; hence, all maize samples were accurately divided into four moldy grades (health, mild, moderate, and severe levels) by determining their catalase activity. The visible and shortwave near-infrared (Vis-SWNIR) and longwave near-infrared (LWNIR) hyperspectral images were investigated to jointly identify the moldy levels of maize. Spectra and texture information of each maize sample were extracted and used to build the classification models of maize with different moldy levels in pixel-level fusion and feature-level fusion. The result showed that the feature-level fusion of spectral and texture within Vis-SWNIR and LWNIR regions achieved the best results, overall prediction accuracy reached 95.00% for each moldy level, all healthy maize was correctly classified, and none of the moldy samples were misclassified as healthy level. This study illustrated that two hyperspectral image systems, with complementary spectral ranges, combined with feature selection and data fusion strategies, could be used synergistically to improve the classification accuracy of maize with different moldy levels.