The research of the Seed germination progress could provide important scientific information and corresponding database for food crops. As one of the primary agricultural products, mung bean is nutrients-rich and can be eaten directly, manufactured as products or cultured to bean sprouts. In order to study the changes of metabolites in plants during the process of metabolism, we extracted the metabolites from the germination samples of mung bean seeds at 24 h, 36 h and 48 h, and analyzed the changes of metabolites in mung bean seeds by ¹H-NMR. Except for its non-destructive and stable characteristics, ¹H-NMR still has some shortcomings of low sensitivity and low resolution in the spectrum. In complex systems, there is overlap in spectrum bands for different compounds, which makes it difficult to give enough information on metabolites. Therefore, chemometric methods are needed to interpret the information in NMR spectroscopy. In this paper, multivariate curve resolution-alternating least squares (MCR-ALS) was used for data processing and analysis of the metabolite data based on NMR. MCR is a bilinear model, which can decompose the given data matrix to the pure spectra and their corresponding relative concentration. MCR can provide physical and chemical meaningful results, which facilitate the analysis of metabolites based on the corresponding spectral library and provide their concentration changes. In this paper, besides the non-negative constraints, selectivity constraint was also used in MCR iteration to reduce the rotation ambiguity in MCR modeling. The changes of metabolites and differential metabolites in mung bean at different germination stages were analyzed. In the determination of samples without certain metabolites, the ¹H-NMR spectra are constrained to zero. From the MCR results, we can find that acetate and choline exist in the pre-germination stage of mung bean, and increasing in the late stage of germination. Sucrose, valine, α-ketoglutarate tryptophan, and phenylalanine inosine do not exist in the pre-germination stage, while they gradually increased during the seed germination of the samples. OMSI, phosphorylcholine and α-glucose exist before the germination and increases in the pre-germination stage. Until the late stage of germination, they were consumed and the content decreased. Lactate, 2-amino-4-oxopentanoic acid, Malic acid, citric acid, choline, stachyose, α-galactose, N1-methylnicotinic acid always exist during the germination of mung bean, and there is no significant change.