The purpose of this study was to investigate the effects of Polygonatum sibiricum (P. sibiricum) on microbial fermentation, physicochemical properties, and functional properties of fermented soymilk. Three types of fermented soymilk were prepared. The first type was fermented directly from regular soymilk (fermented soymilk, FSM), and the other two were fermented after adding P. sibiricum (P. sibiricum fermented soymilk, P-FSM) or P. sibiricum polysaccharides (P. sibiricum polysaccharides fermented soymilk, PP-FSM). The differences in physical and chemical indexes such as pH value, acidity, and water-holding capacity were mainly compared, and the differences in the contents of functional components such as total phenols, total flavonoids, soy isoflavones, γ-aminobutyric acid, and organic acids were compared. The functionalities of the three samples in terms of antioxidant activity were evaluated, and the relevance of each active substance was explored. Compared with the FSM group, the addition of P. sibiricum and P. sibiricum polysaccharides could not only significantly promote the fermentation of Lactobacillus but also significantly improve the stability of the finished products during storage and prolong the shelf life of the finished product. The conversion rates of glycoside soybean isoflavones in the PP-FSM and P-FSM groups were 73% and 69%, respectively, which were significantly higher than those in the FSM group (64%). At the end of fermentation, the γ-aminobutyric acid contents of the PP-FSM and P-FSM groups were 383.66 ± 1.41 mg/L and 386.27 ± 3.43 mg/L, respectively, while that of the FSM group was only 288.66 ± 3.94 mg/L. There were also great differences in the content and types of organic acids among the three samples, especially lactic acid and acetic acid. By comparing the antioxidant capacity of DPPH (1,1-Diphenyl-2-picrylhydrazyl free radical), AB-TS (2,2′-Azinobis-3-ethylbenzthiazoline-6-sulphonate), and iron chelation, it was found that both PP-FSM and P-FSM were superior to FSM, and the antioxidant capacity had a certain correlation with the contents of total phenols and total flavonoids.