Maize is a globally major crop; however, the prevalence of mixed-aged seeds in the market complicates consumer selection and impedes the healthy development of the maize industry. This study introduces a novel method for identifying maize seeds of different storage ages. Seeds were categorized into three age groups: new seeds, one-year stored, and two-year stored, with 300 seeds per group. Hyperspectral images of all 900 samples were acquired using a visible and near-infrared (Vis-NIR) hyperspectral imaging system. To achieve optimal results with minimal spectral data, a feature wavelength selection algorithm based on Inter-Class Feature Differences (IFD) was proposed. When only using the selected three key wavelengths, combined with the linear discriminant analysis (LDA) algorithm, the discrimination accuracy among three different age groups reached 85.67%, while the discrimination accuracy between new and aged seeds achieved 95.33%. Compared to two commonly used variable selection algorithms—Successive Projections Algorithm (SPA) and Random Frog (RF), the proposed IFD method demonstrated superior performance when only a limited number of key wavelengths were used for modeling. These results indicate that the proposed algorithm offers an effective and efficient solution for maize seed age discrimination, showing great potential for practical application.