This paper further investigates the effects of silica base pore size and the molecular weight of polyethylene glycol (PEG) ligands on the coverage of PEG-bonded phases, as well as the resolution of protein separation in high-performance hydrophobic interaction chromatography (HPHIC). The results demonstrate that among the PEG-bonded phases examined in this study, the bonded phase coupled PEG-1500 on LiChrospher 500 silica exhibited the best resolution in protein separation.