The precise identification of maize kernel varieties is essential for germplasm resource management, genetic diversity conservation, and the optimization of agricultural production. To address the need for rapid and non-destructive variety identification, this study developed a novel interpretable machine learning approach that integrates low-field nuclear magnetic resonance (LF-NMR) with morphological image features through an optimized support vector machine (SVM) framework. First, LF-NMR signals were obtained from eleven maize kernel varieties, and ten key features were extracted from the transverse relaxation decay curves. Meanwhile, five image morphological features were selected using the recursive feature elimination (RFE) algorithm. Before modeling, principal component analysis (PCA) was used to determine the distribution features of the internal components for each maize variety. Subsequently, LF-NMR features and image morphological data were integrated to construct a classification model and the SVM hyperparameters were optimized using an improved differential evolution algorithm, achieving a final classification accuracy of 96.36%, which demonstrated strong robustness and precision. The model’s interpretability was further enhanced using Shapley values, which revealed the contributions of key features such as Max Signal and Signal at Max Curvature to classification decisions. This study provides an innovative technical solution for the efficient identification of maize varieties, supports the refined management of germplasm resources, and lays a foundation for genetic improvement and agricultural applications.