To effectively realize the resource utilization of dredged silt in river channels, this study used dredged silt as the main raw material, supplemented with different proportions of organic materials (distiller's grains, cassava residue, and mushroom residue), and developed different rice seedling nutrition soil formulas. By comparing the differences in physicochemical properties of these nutrient soils and their effects on rice seedling quality, and using principal component analysis to comprehensively evaluate the growth indicators of rice seedling, the optimal nutrient soil formulas were screened out. The results showed that, compared with pure silt, adding organic materials to silt significantly reduced the pH value and bulk density of nutrient soil, while significantly increased electrical conductivity (EC), total porosity, organic matter and available phosphorus content. In the consective two seasons of seedling cultivation experiment, the treatments of adding organic materials to silk generally showed better seedling growth than the pure silk treatment, but there were differences in the effectiveness between the treatments. In the first season experiment, the treatment with 40% distiller's grains added to the silt showed the best seedling rate and plant height performance, which were 85.79% and 18.33 cm, respectively. The treatment with 20% cassava residue added to the silt showed the best performance in terms of SPAD value, total root length, and aboveground dry matter weight of 100 plants, reaching 29.52 cm, 81.63 cm, and 2.10 g, respectively. In the second season experiment, the treatment with 40% distiller's grains added to the silt had the highest leaf age, plant height, and stem-based width, which were 4.49, 23.10 cm, and 2.39 mm, respectively. The treatment with 20% cassava residue added to the silt had the highest underground dry matter weight of 100 plants, reaching 1.28 g. The results of principal component analysis showed that the treatment of adding 40% distiller's grains or 20% cassava residue to silk resulted in better comprehensive quality of machine transplanted seedlings, which could be considered as the suitable formula for rice seedling nutrient soil.