With an objective to understand the differences in the behavior of monocationic and dicationic ionic liquids (ILs) in their interaction with protein, we have investigated the binding interaction of lysozyme enzyme with two monocation ionic liquids (MILs), [C3MIm][Br], [C6MIm][Br], and one dicationic ionic liquid (DIL), [C6(MIm)2][Br]2, by exploiting various experimental methods. These ILs are purposefully chosen so that the effect of both hydrophobicity and structural arrangements of the cationic moiety of ionic liquids (ILs), if any, on the interaction event is understood. Both average ensemble and single molecule pathways have been adopted to obtain a comprehensive picture. For ensemble averaged measurements, the interaction events have been investigated by steady-state and time-resolved fluorescence spectroscopy, whereas for single molecule measurements, fluorescence correlation spectroscopy (FCS) has been utilized. Additionally, the behavior of protein in the absence and presence of ILs has also been investigated through circular dichroism (CD) measurements. The investigations have revealed that MILs and DIL interact differently with the protein. In particular, as compared to MILs, the influence of DIL toward protein is observed to be significantly less in terms of change in the structure and dynamics of protein. The outcome of the present work has demonstrated that imidazolium-based DIL can be a better choice over MILs for retaining native structure of protein in aqueous medium.