A VIS/NIR hyperspectral imaging system was used to classify three different degrees of freeze-damage in corn seeds. Using image processing methods, the hyperspectral image of the corn seed embryo was obtained first. To find a relatively better method for later imaging visualization, four different pretreatment methods (no pretreatment, multiplicative scatter correction (MSC), standard normal variation (SNV) and 5 points and 3 times smoothing (5-3 smoothing)), four wavelength selection algorithms (successive projection algorithm (SPA), principal component analysis (PCA), X-loading and full-band method) and three different classification modeling methods (partial least squares-discriminant analysis (PLS-DA), K-nearest neighbor (KNN) and support vector machine (SVM)) were applied to make a comparison. Next, the visualization images according to a mean spectrum to mean spectrum (M2M) and a mean spectrum to pixel spectrum (M2P) were compared in order to better represent the freeze damage to the seed embryos. It was concluded that the 5-3 smoothing method and SPA wavelength selection method applied to the modeling can improve the signal-to-noise ratio, classification accuracy of the model (more than 90%). The final classification results of the method M2P were better than the method M2M, which had fewer numbers of misclassified corn seed samples and the samples could be visualized well.