Abstract: As an important primary producer, submerged macrophytes regulate the material circulation and energy flow of the ecosystem, but the recovery process of submerged macrophytes is often plagued by sediments with high organic matter load. The effect of plant growth-promoting rhizobacteria (PGPR) on Vallisneria natans (V. natans) growth and its relationship with sediment nitrogen and phosphorus was studied by inoculating strains PC2 (Bacillus stratosphericus), H19 (Bacillus subtilis) and L3 (Bacillus cereus) under high sediment organic matter load. The results showed that PGPR inoculation significantly promoted the growth of V. natans and the comprehensive effects was PC2>H19>L3. The growth of V. natans grown in the non-inoculated treatment was inhibited. The height, root length, fresh weight of aboveground and underground tissues of V. natans in PC2 treatment group increased by 165.0%, 17.4%, 378.8% and 165.1%, respectively. Through RDA analysis and Pearson correlation analysis, the increment of plant growth index were significantly negatively correlated with the increment of Inorg-N, NO₂-N, NO₃-N, Inorg-P and Fe/Al-P in the sediment, indicating their potential control sediment Inorg-N and Inorg-P. Therefore, PGPR inoculation is a certain prospective way to solve the problems of submerged macrophytes recovery and internal pollution.