Excessive discharge of the refractory organic pollutants endangers the development of the society and economy, thus seeking an efficient wastewater abatement method is an urgent need. Herein, Iron (Ⅱ) sulfide (FeS) was employed as the heterogeneous catalyst and coupled with underwater bubbling plasma (UBP) for the elimination of the refractory organic pollutant, malachite green (MG). FeS catalyst was synthesized using the solvothermal method and subsequently characterized comprehensively, focusing on its microstructure, specific surface area, chemical bonds and elements valence states. The UBP system combined with FeS (UBP/FeS) exhibited the robust synergism with a maximum synergistic factor of 1.89. The MG degradation percentage and rate constant were up to 94.7% and 0.237 min−1 within 12 min. The parameter experiments revealed that FeS dosage, pulse frequency, initial MG concentration and solution conductivity of 150 mg/L, 56 Hz, 5 mg/L and 21.8 μS/cm, respective, were more conducive for MG elimination. The MG removal efficiency reached 86.2% after five consecutive applications of FeS. Reactive substances including ·OH, ·O2−, eaq, O3 and H2O2 were confirmed to contribute to MG elimination. Additionally, the conversion circle between ≡ Fe(Ⅱ) and ≡ Fe(Ⅲ) promoted the catalytic conversion of H2O2 and O3 into ∙OH. The comparison of UV–vis spectra and total organic carbon of MG solution before and after reaction revealed the superior degradation of MG in the UBP/FeS system. Hypotheses regarding to the decomposition pathways of MG were formulated based on the identified intermediates. The toxicity level of MG solution was lightened after reaction. The above results indicate that UBP/FeS has the advantages of quick degradation and high efficiency, representing a promising approach for refractory pollutants treatment.