This study delves into the use of compact near-infrared spectroscopy instruments for distinguishing between different varieties of barley, chickpeas, and sorghum, addressing a vital need in agriculture for precise crop variety identification. This identification is crucial for optimizing crop performance in diverse environmental conditions and enhancing food security and agricultural productivity. We also explore the potential application of transformer models in near-infrared spectroscopy and conduct an in-depth evaluation of the impact of data preprocessing and machine learning algorithms on variety classification. In our proposed spectraformer multi-classification model, we successfully differentiated 24 barley varieties, 19 chickpea varieties, and ten sorghum varieties, with the highest accuracy rates reaching 85%, 95%, and 86%, respectively. These results demonstrate that small near-infrared spectroscopy instruments are cost-effective and efficient tools with the potential to advance research in various identification methods, but also underscore the value of transformer models in near-infrared spectroscopy classification. Furthermore, we delve into the discussion of the influence of data preprocessing on the performance of deep learning models compared to traditional machine learning models, providing valuable insights for future research in this field.