The classification of GM and non-GM maize kernels is fundamental for further analysis of the gene action in maize. Therefore, a complete and novel detection scheme based on near-infrared spectra was designed to distinguish GM and non-GM maize kernels. Hyperspectral images (935–1720 nm) of 777 maize kernels from 3 kinds were captured, and the average spectra of the maize kernels were extracted for modeling analysis. The classical modeling methods based on feature engineering were first studied, and the backpropagation neural network–genetic algorithm model showed the best performance with a prediction accuracy of 0.861. Then, novel modeling methods based on deep learning were developed. To dig out the interactive information between different bands and match the application scenarios, the original spectra were transformed into two-dimensional matrices before establishing the deep learning models. A modified convolution neural network (i.e., VGG net) with dilated convolution was finally constructed to classify the maize kernels, and the prediction accuracy reached 0.961. This research provides a referential and novel way to detect GM maize kernels. Future research will improve the detection scheme for monitoring unauthorized GM organisms by introducing the visualization technology of deep learning.