Antimicrobial resistance has become a serious threat to global health. New antimicrobials are thus urgently needed. Ionic liquids (ILs), salts consisting of organic cations and anions with melting points less than 100°C, have been recently found to be promising in antimicrobial field as they may disrupt the bacterial wall and membrane and consequently lead to cell leakage and death. Different types of antimicrobial ILs are introduced in the review, including cationic, polymeric, and anionic ILs. Being the main type of the antimicrobial ILs, the review focuses on the structure and the antimicrobial mechanisms of cationic ILs. The quantitative structure-activity relationship (QSAR) models of the cationic ILs are also included. Increase in alkyl chain length and lipophilicity is beneficial to increase the antimicrobial effects of cationic ILs. Polymeric ILs are homopolymers of monomer ILs or copolymers of ILs and other monomers. They have great potential in the field of antibiotics as they provide stronger antimicrobial effects than the sum of the monomer ILs. Anionic ILs are composed of existing anionic antibiotics and organic cations, being capable to enhance the solubility and bioavailability of the original form. Nonetheless, the medical application of antimicrobial ILs is limited by the toxicity. The structural optimization aided by QSAR model and combination with existing antibiotics may provide a solution to this problem and expand the application range of ILs in antimicrobial field.