Pathogen capture and removal from whole blood is a new strategy for extracorporeal blood purification, especially in initial treatment of sepsis before pathogen identification. Herein, hemocompatible magnetic particles with broad-spectrum bacteria capture capability were proposed for pathogen removal from whole blood, omitting the necessity of pathogen identification. Firstly, we designed and synthesized a new kind of imidazolium-based ionic liquid with good antibacterial activity, and polydopamine coating was utilized as a hemocompatible platform to immobilize ionic liquids on Fe3O4 nanoparticles, forming the hemocompatible magnetic particles (Fe3O4@PDA-IL). The magnetic particles exhibited good hemocompatibility and performed well in the removal of various species of clinically significant pathogens from human whole blood, including S. aureus, E. coli., and the hard-to-treat bacteria of P. aeruginosa and Methicillin-resistant S. aureus, which are the most common pathogens in bloodstream infections. Besides, the Fe3O4@PDA-IL particles were also capable to remove bacterial endotoxins from blood, inhibiting further aggravation of sepsis. Overall, we demonstrated the application of hemocompatible magnetic particles in the removal of pathogens and bacterial endotoxins from whole blood via electrostatic and hydrophobic interactions, without significant effects on blood cells or the activation of coagulation and complement, addressing the feasibility of using imidazolium-based ionic liquids for bacteria capture and removal from whole blood. It would contribute to the development of magnetic separation-based approaches to remove bacteria and bacterial endotoxin for extracorporeal blood purification, especially in initial sepsis therapy before pathogen identification. (C) 2020 Elsevier Inc. All rights reserved.