Taking Sagittaria pygmaea Miq. as the research object, this study investigated its remediation effect on contaminated sediment based on the structural equation model, and meanwhile examined the impacts of sediments with different properties (paddy soil, black odor sediment, nitrate treated sediment, and low water level treated sediment) on the growth of Sagittaria pygmaea Miq.. The results showed that: planting submerged plants significantly promoted the removal of pollutants in sediments; in terms of plant growth, the extremely high concentrations of sulfide, total nitrogen (TN), and total organic carbon (TOC) in the black odor sediment group led to the death of Sagittaria pygmaea Miq. in this group at the early stage of the experiment (on the 5th day). The biomass increment of Sagittaria pygmaea Miq. in the low water evel group and the nitrate group was significantly higher than that in the paddy soil group, indicating that black odor sediment treated with nitrate or under low water level is more suitable for the growth of Sagittaria pygmaea Miq. than paddy soil, with TOC, TN, and total phosphorus (TP) being the main factors affecting plant growth; regarding the interaction mechanism, there was a significant negative feedback relationship between the growth of submerged plants and the pollutant content in sediments, which suggests that implementing phytoremediation within a specific threshold range can achieve a synergistic effect of plant growth and sediment purification. However, the system balance will be disrupted when pollutants exceed the threshold; TN, sulfide, and TOC had the most significant inhibitory effects on plant growth, while TP, due to its relatively weak inhibitory effect on plant growth, was removed during the optimization process of the structural equation model.