In contemporary agriculture, enhancing the efficient production of crops and optimizing resource utilization have become paramount objectives. Garlic growth and quality are influenced by various factors, with fertilizers playing a pivotal role in shaping both aspects. This study aimed to develop classification models for distinguishing garlic fertilizer application differences by employing statistical and machine learning techniques, such as partial least squares (PLS), based on data acquired from a ground-based hyperspectral imaging system in the agricultural sector. The garlic variety chosen for this study was Hongsan, and the fertilizer application plots were segmented into three distinct sections. Data were acquired within the VIS/NIR wavelength range using hyperspectral imaging. Following data acquisition, the standard normal variate (SNV) pre-processing technique was applied to enhance the dataset. To identify the optimal wavelengths, various techniques such as sequential forward selection (SFS), successive projections algorithm (SPA), variable importance in projection (VIP), and interval partial least squares (iPLS) were employed, resulting in the selection of 12 optimal wavelengths. For the fertilizer application difference model, six integrated vegetation indices were chosen for comparison with existing growth indicators. Using the same methodology, the model construction showed accuracies of 90.7% for PLS. Thus, the proposed model suggests that efficient regulation of garlic fertilizer application can be achieved by utilizing statistical and machine learning techniques.