In this study, changes in the basic composition and structural characterisation of water-soluble pectin (WSP), homogalacturonan (HG) and rhamnogalacturonan-I (RG-I) from pomegranate peel were investigated after high-pressure-homogenisation (HPH) at 50 MPa and 300 MPa. The interactions between three pectin and anthocyanin (ACN) complex were also studied. The three pectin fractions were mainly composed of galacturonic acid (34.95%–87.69%), all with low degrees of methyl-esterification ≤41.20%. HPH at 300 MPa increased the binding ratios of ACN to three pectin fractions by 34.22%–34.59%. Changes in the structural characterisation results of pectin confirmed that the depolymerisation and breakdown of the side chains of pectin after HPH promoted electrostatic interactions, hydrogen bond and hydrophobic interaction between pectin and ACN. Correspondingly, the thermal and storage stabilities of ACN in the complex was boosted after HPH at 300 MPa. This study provides insights into the interaction between pectin and ACN under HPH.