When non-seed materials are mixed in seeds or seed varieties of loll value are mixed in high value varieties, it will cause losses to growers or businesses. Thus, the successful discrimination of seed varieties is critical for improvement of seed ralue. In recent years, convolutional neural networks (CNNs) have been used in classification of seed varieties. The feasibility of using multispectral imaging combined with one-dimensional convolutional neural network (1D-CNN) to classify pepper seed varieties was studied. The total number of three varieties of samples was 1472, and the average spectral curve between 365nm and 970nm of the three varieties was studied. The data were analyzed using full bands of the spectrum or the feature bands selected by successive projection algorithm (SPA). SPA extracted 9 feature bands from 19 bands (430, 450, 470, 490, 515, 570, 660, 780, and 880 nm). The classification accuracy of the three classification models developed with full band using K nearest neighbors (KNN), support vector machine (SUM), and 1D-CNN were 85.81%, 97.70%, and 90.50%, respectively. With full bands, SUM and 1D-CNN performed significantly better than KNN, and SVM performed slightly better than 1D-CNN. With feature bands, the testing accuracies of SUM and 1D-CNN were 97.30% and 92.6%, respectively. Although the classification accuracy of 1D-CNN was not the highest, the ease of operation made it the most feasible method for pepper seed variety prediction.