By using lysozyme, hemoglobin (bovine), and pepsin as the model proteins and copolymer F1110 containing reactive functional groups of amido, sulfonate, and carboxylic acid groups as the flocculating agents, selective precipitation of proteins was performed by using two chemical processes. The experiment shows that the surface charge of copolymer F1110 is closely related to the pH value in solution. The flocculation behaviors of proteins with F1110 can be controlled completely by adjusting pH value in solution, which realizes the selective separation of mixed proteins. In addition, the selective precipitation of the proteins is promoted by a "modified flocculation" process, in two steps with a combination of F1110 and polyacrylamide. The characterization of modified flocculation is closely related to the property of the protein. These studies show a great prospect for selectively separating proteins from a mixture solution using designed polyelectrolytes containing reactive functional groups.