Effect of pectin structure on the properties of pectin-β-casein complex systems was investigated in this study. Six types of pectin （L13， L101， L102， L104， H121 and H150） with different structures （galacturonic acid content GA， degree of methoxylation DM， degree of amidation DA， molecular weight Mw） were combined with β-casein， and methods including dynamic light scattering， zeta potential， fluorescence spectroscopy and circular dichroism were applied to determine particle size， zeta-potential， secondary structure， solubility， emulsifying and foaming ability of pectin-β-casein complex systems. Finally， multiple linear regression analysis was used to evaluate the contributions of various pectin structure to the properties of pectin-β-casein complex systems. The results showed that electrostatic interaction was occurred between pectin and β-casein resulting in forming complexes， and addition of pectin changed molecular structure of β-casein. Pectin-β-casein complexes have higher emulsifying ability and foaming ability than β-casein. Multiple linear regression revealed that solubility and emulsification were positively correlated with GA， DM and DA， but negatively correlated with Mw. DA had the greatest effect on solubility and emulsifying properties， and they were minimally affected by Mw. The foaming ability was positively correlated with GA and DM， but negatively correlated with DA and Mw. DA has the greatest impact on foaming ability， and Mw has the least impact on it.