Rebaudioside A (RA) and Stevioside (STV) are abundant steviol glycosides (SGs) contained in Stevia rebaudiana Bertoni leaves, which exhibit good stability and various pharmacological activities that have been widely developed in the food and pharmaceutical industries. However, the stevia industry still suffers from high consumption, low efficiency, and long-term dependence on the operational experience of workers. The extraction process of Stevia rebaudiana Bertoni leaves one of the fundamental units for the production of SGs, which is crucial for the homogeneous stability of the final product. The applications of near-infrared (NIR) spectroscopy combined with chemometrics in determining the end-point of the extraction process were proposed in this study. Firstly, the quantitative models were established by partial least squares regression (PLSR) and back-propagation artificial neural network (BP-ANN) to rapidly detect the changes of content RA and STV, which have good prediction results. Secondly, the qualitative analysis methods were established by moving block of standard deviation (MBSD), absolute distance of standard deviation (ADSD) and principal component analysis (PCA) to rapidly determine the extraction end-point, which MBSD method was consistent with the high-performance liquid chromatography (HPLC) method. Finally, the variation of the extraction process was revealed by Aquaphotomic to provide a microscopic perspective of water molecules for end-point determination. The HPLC method requires 30 min to determine the content, whereas NIR spectroscopy requires only 18 s to obtain a spectrum. These results indicate that the extraction end-point of Stevia rebaudiana Bertoni leaves can be determined rapidly and accurately using NIR spectroscopy, which provides a significant reference for other food, medicinal plants, and agricultural products production processes.