Protein crystallization is a complex physical and chemical process. The high-quality protein crystal is still a persistent bottleneck to the application of X-ray crystallography in structural biology. The additives may promote formation of crystal nucleus and subsequent growth in protein crystallization. As a distinct material, ionic liquids (ILs) have aroused great attention and interest for protein crystallization due to their unique properties. We reviewed the progress of protein crystallization and reported research about protein crystal morphology control by ILs, as crystal growth template, in aqueous solutions. ILs encourage changes in some cases in terms of growth morphology and crystal size. The effect of ILs on lysozyme growth morphology can be attributed to changing interaction among lysozyme molecules in aqueous solutions. This work can provide some initial insight into the preparation of high quality crystal and the development of new crystal form.