Mercury (Hg) pollution in soil has grown into a severe environmental issue. Effective in situ immobilization techniques are crucially demanded. In this study, we explored the application of carboxymethyl cellulose stabilized iron sulfide nanoparticles (CMC-FeS) for in situ immobilization of Hg in soil. CMC-FeS (a CMC-to-FeS molar ratio of 0.0004) was prepared via the reaction between FeSO4 and Na2S using CMC as a stabilizer. Remedying the Hg-polluted soil using 0.03 % CMC-FeS via batch experiments effectively reduced the acid leachable Hg by 97.5 % upon equilibrium after 71 days. Column elution tests demonstrated that the addition of CMC-FeS decreased the peak Hg concentration by 89.9 % and the total Hg mass eluted by 94.9 % after 523 pore volumes. CMC-FeS immobilized Hg in soil via chemical precipitation, ion exchange, and surface complexation. After the CMC-FeS treatment, Hg was transformed from more available exchangeable, carbonate-bound, and organic material-bound forms into the less available residual fraction, reducing the environmental risk of soil Hg from medium to low. The application of CMC-FeS boosted the soil enzyme activities and enhanced the soil bacterial diversity whereas decreased the production of methylmercury. CMC-FeS also facilitated long-term immobilization of Hg in soil. The acid leachable Hg and relative Hg bioaccessibility was decreased. Lift cycle assessment indicated that the preparation and application of CMC-FeS for in situ Hg remediation in soil met green chemistry principles. The present study confirms that CMC-FeS can be applied as an efficient and “green” amending agent for long-term Hg immobilization in soil/sediment.