Coarse-grained Monte Carlo simulations have been applied to study complex coacervation of pectin with bovine serum albumin (BSA) and two isomers of beta-lactoglobulin (BLGA and BLGB). The influence from the specific distribution of charge and hydrophobic patches in protein surfaces on the self-association of proteins and their complex coacervation were investigated. A simple and direct method to quantify the contribution of hydrophobic interaction on protein complex formation was introduced. Highly accordant pH dependence of charges in proteins and phase boundaries for the complex coacervation was observed Comparing to BSA, beta-lactoglobulin had a higher probability and a broader pH window to form complex coacervate. The major cause is the higher self association proneness of beta-lactoglobulin, as evidenced by the more negative second virial coefficients. The double-point mutations of G64D/V118A from BLGB to BLGA caused the latter one to have a stronger self-association proneness. It was revealed that the larger negative charge patch in BLGA synergistically enhanced the attraction of the strongest binding site, a positive charge patch, when pH was close to or above the isoelectric point of the protein. These findings suggest that the coarse gained simulation is competent to explore the delicate influences from different proteins in protein-polysaccharide complex coacervates.