Abstract: Texture is one of the most critical quality attributes to directly influence consumer acceptance of frozen foods. Controlling ice crystal growth is an effective strategy to regulate the texture of frozen materials. It is essential to explore the inhibitory effect of pectin's structure on ice recrystallization in the formulation design. Particularly, the quality of frozen products can be preserved during storage and thawing. Pectin, a natural polysaccharide commonly found in plant cell walls, has demonstrated significant inhibition effects on ice crystals; However, the structure-activity relationship behind them still remains unclear. This study aimed to investigate the influence of pectin esterification and amidation on ice crystal inhibition. Pectin was constructed with varying degrees of esterification and amidation using enzymatic de-esterification and amidation modifications. Splat tests and molecular dynamic (MD) simulations were employed to delineate the potential mechanisms, by which methyl esterification and amidation of pectin are influenced by ice crystal growth. The results indicated that the lower esterified pectin shared the stronger ice recrystallization inhibition (IRI), whereas the amidation diminished the IRI capability. Specifically, the average diameter of the largest ice crystals was 29.19 μm in 51% esterified Pectin, approaching that in a sucrose solution (mean largest grain size, MLGS, 19.4% larger). MD simulations revealed that the number of ice molecules in different systems of amidated pectin reached equilibrium around 52 ns, while the ice crystal growth in pectin with varying degrees of esterification concluded later, reaching completion at 62 ns. A more robust ability of pectin was achieved with the lower esterification degrees to inhibit ice crystal growth. The amidated pectin chains were adopted as a concave shape when spliced with adjacent periodic images. Ice crystals tended to grow preferentially along the sides of amidated pectin. There was no observed in Pectin with different degrees of esterification. Therefore, the amidated pectin reduced the contact surface with ice crystals, leading to being enveloped by the growing ice interface. There was a higher interaction energy between pectin and water molecules. An increasing number of hydrogen bonds then led to the tighter association for the strong inhibition of ice crystal growth. Consequently, the pectin with a lower degree of esterification shared the stronger interactions with water molecules, and then hindered their binding to ice crystal growth interfaces, thus facilitating ice crystal inhibition. There were three impacts of esterification and amidation degrees on the inhibition mechanisms of the ice crystal growth, including: 1) hydrophilic groups, such as hydroxyl and carboxyl, of pectin were bound to the ice crystal growth interface, while hydrophobic groups, such as methyl, inhibited the attachment of water molecule; 2) Hydrophilicity of pectin was enhanced its interaction with water molecules, thereby inhibiting their migration; 3) Alterations in pectin hydrophilicity were resulted in the conformational changes at the ice crystal growth interface, thus affecting the contact area with ice crystals. These findings were significant implications for the more effective design and formulation of frozen food products, leading to the high texture, stability, and quality. The insights were greatly contributed to a better understanding of mechanisms behind pectin's IRI activity, in order to explore other polysaccharides and their derivatives. Novel cryoprotectants can be expected for the various industrial applications in the high quality and shelf life of frozen foods, particularly on the consumer preferences for healthier and natural ingredients.