As a green and safe food and drug ingredient, stevia has broad application prospects. However, moisture absorption is a major problem it faces, which is also a common problem in most preparations raw materials. Research and analyze the process state of moisture absorption, then proposed targeted solutions have important theoretical significance and application value. Near-infrared spectroscopy analysis technology combined with chemometric methods were used to analyze the moisture absorption process of stevia in this study. On this basis, the External Parameter Orthogonalisation (EPO) algorithm was used to eliminate the influence of sample moisture, and to establish a rapid analysis method for Rebaudioside A (RA) content in stevia. The results showed that at the beginning of the moisture absorption process of stevia, water molecules were rapidly adsorbed on the surface of the stevia powder to form a monomolecular layer; after that, the surface adsorption sites became fewer, the moisture absorption rate became significantly slower, and water molecules would be adsorbed on top of the monomolecular layer at the same time; finally, the overall moisture absorption of stevia reached its saturated state, and the water content remained stable. After revealing the law of moisture absorption, the RA quantitative model was established using the spectrum preprocessed by the EPO algorithm, the root mean square error, coefficient of determination, and predicted relative standard deviation of the external test set of the model were 0.669 5%, 0.957 0 and 4.336 8, respectively. Compared with the model built before EPO treatment, there was a big improvement, indicating that the EPO algorithm could effectively remove the influence of moisture absorption. In this study, near infrared spectroscopy was used for the first time to characterize the water changes during the moisture absorption of stevia, at the same time, the EPO algorithm was used to effectively eliminate the influence of moisture absorption and realize the rapid determination of RA in stevia products, which provides a reference for its further research and use.