Regulation of defected metal-organic frameworks (MOFs) is a promising strategy to improve their performances. Ionothermal synthesis method provides extra opportunities to overcome the confinement of traditional DMF-based solvent-thermal syntheses. In this study, ionic liquid 1-ethyl-3-methylimidazolium acetate [EMIM]OAc was employed to synthesize UiO-66 and UiO-66-NH2 by ionothermal synthesis. Characterization results indicate that UiO-66 synthesized in ionic liquid exhibits high miss linker defects at modulator-free conditions. The properties of obtained UiO-66, such as particle sizes, specific surface area, and pore size, were greatly correlated with the usage of acetic acid modulator. The particle sizes of UiO-66-IL, UiO-66-20eq, UiO-66-50eq and UiO-66-100eq were 195.6, 214.8, 231.0, and 142.4 nm, respectively. Moreover, in the adsorption experiments for organic dyes (Rhodamine B), the defected UiO-66 with high miss linker defects exhibited remarkable performance in sewage treatment. The adsorption capacity of UiO-66-IL on Rhodamine B was 46.47, 47.47, and 47.65 mg g(-1) at 303, 308, and 313 K, respectively. Our study provided a rational method in defects regulation of MOFs and guidance for future property optimization of MOFs materials.