Structural design of high-performing catalysts for boosting refractory organic pollutants degradation remains a great challenge. Herein, a natural wood-derived catalyst comprising of wood carbon and Fe/Co sites was proposed as the peroxymonosulfate (PMS) activator to enhance ciprofloxacin (CIP) pollutant degradation. The bimetallic Fe/Co sites were highly dispersed and stabilized on carbon surface. The carbon-based catalyst achieved 100% removal rate for CIP within 4 min. After four consecutive cycles, the removal rate still reached 92.8%, displaying separable and reusable ability of this catalyst. The carbon-based catalyst could also exhibit excellent degradation performance under a wide pH range of 2.0–8.0. Density functional theory (DFT) calculation revealed that Fe/Co sites at wood carbon had the high adsorption energy and induced interfacial electron transfer for enhanced breakage of O–O bond. The sulfate radical (SO4•−), hydroxyl radical (•OH) and singlet oxygen (1O2) were main reactive oxygen species and their relative contribution was calculated to be 13.51%, 17.54% and 68.95%, respectively. The formed by-products and intermediates had almost no toxicity. This work proposes a new structural design of wood carbon-based system for enhancing antibiotic pollutant in aqueous environment, which facilitates the development of wastewater treatment technology.