In this study, humic substances (HS) selected from 8 composting groups (peanut straw, sesame straw, corn straw and deciduous leaves, with or without grape marc) were used to remove Cd and Ni from artificially contaminated sediments. Sesame straw compost appeared to have the highest removal capacity for heavy metals through a series comparison on Cd removal efficiency, yield of HS and fulvic acids (FA), and seed germination index. The selected sesame HS was further used to wash two contaminated sediments of varying properties (a clay type for sediment 1 and a silty loam for sediment 2). Batch desorption experiments were conducted to determine the optimum HS concentration, equilibrium time, pH, solid-to-liquid ratio, and washing frequency. Under optimum conditions, a triple washing removed 74.16% of Cd and 42.91% of Ni from sediment 1, and 86.88% of Cd and 43.84% of Ni from sediment 2, respectively, whereas a commercial FA only achieved half of the efficiency. After washing, both sediments were identified with increased contents of total organic matter total nitrogen and phosphorus. Therefore, HS from the sesame straw compost is a cost-effective, efficient and environmental-friendly washing agent to remove heavy metals from contaminated sediments.