Precipitation of soluble proteins in fermentation broth with addition of water-soluble polymers is an important method for downstream processing in biochemical technology. In the present work, the chemical features of "modified flocculation" are explored with lysozyme as the model protein to be precipitated with polyacrylamide in combination of an anionic copolymer containing reactive functional groups. The protein first interacts with low molecular weight anionic copolymer at gentle agitation, followed by precipitation with addition of high molecular weight polyacrylamide. The data on protein recovery in terms of light absorbance (280 nm) are analyzed to shed light on the mechanism of flee formation. The size distribution of the flocs was determined and the effects of the structure of the copolymer on the mechanism of flocculation were investigated. The results support the description of "modified flocculation", which enriches the interaction between protein and polymer, and leads to formation of protein-polymer flocs large enough to precipitate easily in water.