Research Highlights: We firstly interpreted nutritional mechanisms involved in growth regulation and phytochemical accumulation in Cyclocarya paliurus (Batal.) Iljinskaja under three inoculant types, and selected bacterial inoculations for multiple purposes of C. paliurus plantation. Co-inoculation with phosphate-solubilizing bacteria (PSB) and N2-fixing bacteria (NFB) performed better in growth promotion and nutrient uptake than single bacterial inoculation. Background and Objectives: C. paliurus is a well-known medicinal plant as it accumulates bioactive compounds (BC) such as flavonoids, triterpenoids, and polysaccharides, in its leaves. However, the effects of plant growth-promoting rhizobacteria (PGPR) on the growth and BC yields in C. paliurus are not known. To fill this gap, the effects of different inoculants should be examined. Materials and Methods: A pot experiment was conducted and two-year-old C. paliurus seedlings were inoculated with three inoculant types (PSB, NFB, PSB + NFB). After four rounds of inoculation, the growth characteristics and concentrations of flavonoids, triterpenoids, and polysaccharides, as well as the nutrients in soil and leaves, were measured. Results: The inoculations resulted in the elevation of soil available nutrients, with improvements in plant growth, BC yield, and N and P uptake in leaves. However, the changes in BC yields were mainly a result of elevated leaf biomass rather than BC concentrations, and leaf biomass was regulated by C:N:P stoichiometry. Co-inoculation with PSB and NFB was applicable for leaf production, while inocula related to NFB resulted in higher BC yields than PSB and control. Conclusions: Our results implied that bacterial inoculants improved plant growth and BC yield by altering the nutrients in soil and leaves, while three inoculant types showed a different pattern in which co-inoculation with four strains presented a greater performance than single bacterial addition.