The heterogeneous Fenton process is a strategy for overcoming the greatest shortcomings of traditional homogeneous Fenton, i.e. the high generation of ferric hydroxide sludge and effectivity in a limited pH range. In this study, we constructed a heterogeneous Fenton system with natural iron-bearing clay mineral (nontronite) and dimethoxyhydroquinone (DMHQ) to degrade lincomycin (LCM) without the addition of H2O2. The degradation mechanism was derived from the hydroxyl radicals (•OH) produced from the oxygenation of Fe(II) in nontronites, which was reduced by DMHQ. Acidic conditions and low concentrations of LCM were favourable for LCM degradation. When the solution pH increased from 3 to 7, the final LCM removal ratio decreased from 95 to 46%. However, LCM can still be degraded by 46% under neutral conditions and 20% at the LCM concentration of 500 μmol/L. The nontronite has good reusability, and the LCM degradation efficiency in the fourth cycle still exceeded 90% of the original efficiency. The degradation sites of LCM mainly occurred in the methyl thioether moiety and the aliphatic amine group on the pyrrolidine ring, with the final product of CO2. This research presents a new eco-friendly and cost-effective method for the heterogenous Fenton process without external H2O2.