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Deep learning algorithms represented by convolutional neural networks bring new opportunities for spectral analysis technology. Convolutional neural networks are more straightforward than traditional chemometric algorithms for detecting the quality of agricultural products, reducing the procedures of spectral preprocessing and band selection, and with higher prediction accuracy. However, there are few research papers on the relevance of the explanation of the convolutional neural networks model mechanism, and the reader cannot fully understand convolutional neural networks feature learning. In this study, convolutional neural networks combined with the subregional voting method were used to predict the moisture content of semen ziziphi spinosae. Firstly, 10 regions of interest were divided using the subregional voting method, and the results of network models were compared. It was found that the average spectrum of the fifth region of interest had the best prediction of moisture content because it was closest to the central region of semen ziziphi spinosae. Based on this, a convolutional neural network containing three convolutional layers, three pooling layers, and one fully connected layer is proposed. Partial least squares regression, backpropagation neural network, and convolutional neural networks were established to predict the moisture content of semen ziziphi spinosae. The correlation coefficient of the prediction set of the partial least squares regression is 0.98 after the multiplicative scatter correction preprocessed the spectra, and correlation coefficient of the prediction set of the backpropagation neural network is 0.83 after the standard normal variate preprocessed the spectra. The correlation coefficient of the prediction set of the convolutional neural networks established by using the raw spectra reached 0.99. The spectral preprocessing method can improve the prediction set correlation coefficient of partial least squares regression and backpropagation neural network. Still, it will reduce the prediction ability of convolutional neural networks. This study also analyzed the effect of different learning rates on the performance of convolutional neural networks, and it was found that the training loss and training accuracy performed most consistently when the learning rate was 0.01. Secondly, this study also visualized the output feature maps of the three convolutional layers of convolutional neural networks and verified the effectiveness of convolutional neural networks feature band extraction. This study provides new ideas for deep learning in the online detection of seed moisture content.