Ligusticum Chuanxiong, a perennial herb of considerable medicinal value commonly known as Chuanxiong, holds pivotal importance in sliced form for ensuring quality and regulating markets through geographical origin identification. This study introduces an integrated approach utilizing Near-Infrared Spectroscopy (NIRS) and Convolutional Neural Networks (CNNs) to establish an efficient method for rapidly determining the geographical origin of Chuanxiong slices. A dataset comprising 300 samples from 6 distinct origins was analyzed using a 1D-CNN model. In this study, we initially established a traditional classification model. By utilizing the Spectrum Outlier feature in TQ-Analyst 9 software to exclude outliers, we have enhanced the performance of the model. After evaluating various spectral preprocessing techniques, we selected Savitzky–Golay filtering combined with Multiplicative Scatter Correction (S-G + MSC) to process the raw spectral data. This approach significantly improved the predictive accuracy of the model. After 2000 iterations of training, the CNN model achieved a prediction accuracy of 92.22%, marking a 12.09% improvement over traditional methods. The application of the Class Activation Mapping algorithm not only visualized the feature extraction process but also enhanced the traditional model’s classification accuracy by an additional 7.41% when integrated with features extracted from the CNN model. This research provides a powerful tool for the quality control of Chuanxiong slices and presents a novel perspective on the quality inspection of other agricultural products.