The effects of substrates size grading on the purification of black and odorous water by self-designed ecological media boxes and their effects on the accumulation and growth of N and P in aquatic plants were studied by artificial static simulation test. The results showed that with the prolongation of treatment time, the removal rate of each pollutant increased gradually. The removal effect of TP, TN and NH₄⁺-N in both progressively-graded groups, anti-graded group was better than that in single plant group and matrix group. The removal efficiency of TP in progressively-graded group was better than that in anti-gradation group, its removal rate reached 66.9%. The accumulation of TP in progressively-graded group was better than that in anti-gradation group and plant group. But the removal efficiency of TN and NH₄⁺-N in water in anti-graded group was better than those in progressively-graded group, the removal rates reached 69.1% and 87.4% respectively. The accumulation of TN in anti-gradation group was better than those in progressively-graded group and plant group. The plant factors in the ecological media boxes had a low contribution rate to nitrogen and phosphorus removal. The removal of N and P was mainly through non-plant factors (matrix, microbe). However, except for the blank group, there was no significant difference in the removal of COD_Mn between the groups, indicating that the direct removal of COD_Mn by substrates and plants is not obvious, and it depends more on the role of microorganisms attached to the substrate and plant carriers. The experimental group containing the mineral matrix (progressively-graded group, anti-gradation group, and matrix group) could raise the pH of water and effectively regulate the acidic water body. The way in which aquatic plants (Vallisneria natans (Lour.) Hara) were directly implanted into the sediment (plant group) is more suitable for plant growth. Therefore, the effect of repairing water bodies with different N, P pollution levels can be satisfied by replacing the substrates size gradations.