The phase separation of ionic liquids (ILs) in water is studied by laser light scattering (LLS). For the ILs with longer alkyl chains, such as [C8mim]BF4 and [C6mim]BF4 (mim=methylimidazolium), macroscopic phase separation occurs in the mixture with water. LLS also reveals the coexistence of the mesoscopic phase, the size of which is in the order of 100–800 nm. In aqueous mixtures of ILs with shorter alkyl chains, such as [C4mim]BF4, only the mesoscopic phase exists. The mesoscopic phase can be effectively removed by filtration through a 0.22 μm filter. However, it reforms with time and can be enhanced by lowering the temperature, thus indicating that it is controlled by thermodynamics. The degree of mesoscopic phase separation can be used to evaluate the miscibility of ILs with water. This study helps to optimize the applications of ILs in related fields, as well as the recycling of ILs in the presence of water.