Spent mushroom substrate (SMS) as an organic amendment to plant production has received increasing attention on soil phytoremediation. However, organic amendments are known to contribute to greenhouse gas (GHG) emission from soils. Castor oil plant has a high biomass production and phytoremediation potential for heavy metal-contaminated soils. In the present study, the roles of SMS on phytoremediation efficiency of castor oil plant (Ricinus communis L.) from cadmium (Cd) and nickel (Ni)-contaminated soils were investigated, and the impact of SMS application on methane emission from the contaminated soil were evaluated. Pot experiments with SMS-amended and unamended contaminated soils were conducted to investigate Cd and Ni accumulation in R. communis and CH emission. After growing for 3 months in soils with the addition of Cd (10 mg/kg) and Ni (at rates of 200 and 600 mg/kg), the dry biomass and the concentrations of Cd and Ni in the R. communis were measured, and the mobility factors for Cd and Ni were calculated. To assess methane emission, CH fluxes and potential rates of CH production and oxidation were measured pre- and post-incubation. SMS addition significantly improved the growth of R. communis and gave 19.15~82.46% more dry weight as compared to the single plant cultivation in the contaminated soils. SMS also increased plant Cd uptake and the total amount of Cd accumulation in R. communis increased by 28.1-152.1%, respectively, in signal Cd treatment and Cd-Ni complexation treatment, as compared to the single plant cultivation. The high values of mobility factor for Cd in single plant cultivation and co-application of SMS and R. communis pointed to the potential of R. communis to the Cd mobilization from the contaminated soils. Moreover, the addition of SMS tended to stimulate CH uptake that the average increases in CH uptake rate were 3.84-fold (in controls) and 2.91-fold (in single Cd treated soils) by the co-application of SMS and R. communis as compared to the single plant cultivation. The results suggested that the application of SMS could improve the growth of R. communis in Cd and Ni-contaminated soil, enhance heavy metal bioaccumulation, and stimulate soil CH uptake. Therefore, SMS might be useful for enhancing phytoremediation of heavy metals and mitigate CH emission from the contaminated soil. In addition, results in the study implied that implementing carefully designed management strategies (e.g., application of organic residues) during contaminated soil remediation is a promising solution for agricultural waste management and soil phytoremediation.