The process of extracting polyphyllin II and polyphyllin VII by water-assisted extraction was established and optimized in this study. Response surface methodology was used to establish a prediction model to optimize the extraction conditions. Based on the one-way test, the Box–Behnken design with three factors and three levels was used for the experimental program, and the composition analysis was carried out by high-performance liquid chromatography (HPLC). The optimal extraction conditions for polyphyllin II and polyphyllin VII were as follows: extraction time of 57 and 21 min, extraction temperature of 36 and 32 °C, solid-to-liquid ratio of 1:10 and 1:5 g/mL, respectively, and the yields of polyphyllin II and polyphyllin VII were 1.895 and 5.010%, which was similar to the predicted value of 1.835 and 4.979%. The results of the ANOVA showed that the model fit was good, and the Box–Behnken response surface method could optimize the water-assisted extraction of saponins from the leaves of Paris polyphylla var. yunnanensis. This study provides a theoretical basis for the application of polyphyllin II and polyphyllin VII in pharmaceutical production.