Phosphorylation could improve functional characteristics of proteins/peptides, and might be used in the functional improvement of herring egg peptides owing to their enriched phosphorylation sites. The present study aimed to study the effect of phosphorylation on calcium-binding ability of herring egg peptides, and investigate the conformational structure and intermolecular forces of herring egg phosphopeptides (HEPPs)-calcium complex. The HEPPs were found to be superior in calcium-binding activities, as compared to the non-phosphorylated variant. This finding might be attributed to the interaction between calcium ions and the introduced phosphate groups of HEPPs. Calcium favored the formation of β-sheet structure on the HEPPs and induced structural folding, thus assembling into spherical nanoparticles. The conformation of HEPPs-Ca nanoparticles was formed and stabilized mainly by hydrophobic interaction, hydrogen bonds and electrostatic interaction.