In this study, eggplant seeds of fifteen different varieties were selected for discriminant analyses with a multispectral imaging technique. Seventy‐eight features acquired with the multispectral images were extracted from individual eggplant seeds, which were then classified using SVM and a one‐dimensional convolutional neural network (1D‐CNN), and the overall accuracy was 90.12% and 94.80%, respectively. A two‐dimensional convolutional neural network (2D‐CNN) was also adopted for discrimination of seed varieties, and an accuracy of 90.67% was achieved. This study not only demonstrated that multispectral imaging combining machine learning techniques could be used as a high‐throughput and nondestructive tool to discriminate seed varieties but also revealed that the shape of the seed shell may not be exactly the same as the female parents due to the genetic and environmental factors.