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Cellulose and pectin are the key components of plant primary cell walls (PCWs) responsible for their dynamic growth, as they transition from a flexible structure at early stages to a rigid unit at full growth. However, a fundamental understanding of the pectin-cellulose interface and interactions within PCW and the underlying mechanics of these materials remained a subject of debate, hindering progress in bioinspired and sustainable composite designs to meet the demands of emerging fields, from flexible robotics to regenerative medicine. This study presents a multiscale investigation into the CNC-pectin interface and the influence of calcium ion-mediated cross-links, integrating molecular dynamics (MD) simulations, supported by experimental data of molecular interactions via spectroscopic studies and bulk interactions via viscosity measurements. The MD simulations revealed cross-linking mechanisms of “zipper” and “egg-box”, both being present, depending on local composite properties and ionic concentrations, with the zipper model being the dominant mechanism by almost 10 times with relative insensitivity to Ca2+, thus providing deeper insights into the long-ongoing discussion on pectin Ca2+ interactions. The zipper model is driven by the coordination of Ca2+ with deprotonated carboxyl groups (–COO–), while the egg-box model involves both carboxyl and hydroxyl groups (–OH). The confirmation via spectroscopic studies, characterized by consistent shifts in Raman peaks of the carboxylate group, indicating the rearrangement of ester and carboxyl groups of HGA, and concentration-dependent peak enhancement trends of the hydroxyl group in the FTIR study involved in the two models validated the MD outcomes. Furthermore, MD predicted viscosity aligned with bulk properties provides a basis for the future extension of the work on quantifying interface energies. Overall, the study provides fundamental knowledge on Ca2+-mediated CNC-pectin interactions, helping to resolve reported experimental discrepancies and offering design guidelines for advanced pectin-based biocomposites.