It is of great importance to develop novel and sensitive sensing materials for the detection of proteins and microorganisms to fulfill the demand of disease diagnosis. As the selectivity and sensitivity of sensing systems are highly dependent on the receptor, the fluorescent sensor array with imidazolium ionic liquids (ILs) and ionic liquid-quantum dots conjugates as semiselective receptors is developed for protein/bacteria differential sensing or discrimination. The IL sensing system formed by 1,3-dibutylimidazolium chloride (BBimCl), 1,3-diethylimidazolium bromine (EEimBr), 1,3-dibutylimidazolium bromine (BBimBr), 1,3-dihexylimidazolium bromine (HHimBr), and 1,3-dioctylimidazolium bromine (OOimBr) and the IL@QDs/QDs sensing system formed by CdTe, BBimCl@CdTe, EEimBr@CdTe, BBimBr@CdTe, and HHimBr@CdTe are tested, by transferring the interaction binding difference between receptors and proteins to the fluorescent response pattern. The IL sensing system is applied to the identification of 48 samples (8 proteins at 500 nM) with an accuracy of 91.7%. For the IL@QDs/QDs sensing system, 8 proteins are completely distinguished with 100% accuracy at a very low concentration level of 10 nM. Remarkably, 36 training cases (6 strains of bacteria from 3 different species) are discriminated with 100% (OD600 of 0.1).