Covalent organic frameworks (COFs) have attracted tremendous attention due to their excellent performance in wastewater remediation, but their practical application still suffers from various challenges. The development of highly-efficient magnetic COFs along with fast adsorption kinetic and high adsorption capacity is very promising. To achieve the purpose, thiol-functionalized magnetic covalent organic frameworks (M-COF-SH) with abundant accessible chelating sites were designed and synthesized by utilizing disulfide derivative as building blocks and subsequently cutting off the disulfide linkage. After the cutting process, the crystallinity, porosity, superparamagnetism of pristine M-COF are well maintained, and the resultant M-COF-SH turned out to be an effective and selective platform for Hg capture from water. Impressively, the resulting composite exhibited a maximum adsorption capacity of Hg as high as 383 mg g. In addition, it also displays a rapid kinetic, where the adsorption equilibrium can be achieved within 10 min. More importantly, there is no significant loss of its adsorption performance even after recycling 5 times. This work not only offers a reliable platform for wastewater remediation but also provides a conceptual guide to prepare functionalized M-COF composites which cannot be obtained through conventional approaches.