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While the relative abundance of plant biopolymers can vary significantly depending on the cell type and maturation, pectin and cellulose nanocrystals are among the two key biopolymers found in many plants’ primary cell walls at the early growth stage. Nanocomposites that utilize cellulose nanocrystals have gained extensive interest over the years. Limited knowledge regarding pectin and the interaction between pectin and cellulose is available because pectin was considered a non-loading-bearing component with little interaction with cellulose. However, recent developments in primary cell wall structure have shifted, and pectin is viewed as a part of the reinforcement structure. Thus, understanding the role of pectin has become relevant in creating advanced bio-composites that mimic the structure of primary cell walls. This work aims to provide fundamental information on the interaction between pectin and cellulose nanocrystals using molecular dynamics simulations. A dry interaction is modeled to replicate their status in a composite, where water is removed via processing such as freeze-drying. Interphase models consisting of two cellulose nanocrystals and a homogalacturonan pectin molecule are created to simulate the interfacial structure, including binding potential energy and hydrogen bonds. Friction and adhesion responses are predicted by moving one cellulose nanocrystal against the other. The results show that a pectin molecule increases the friction at the interphase by 14 and 8 times between CNC (200) and (110) surfaces, respectively, which is correlated to the significantly increased binding energies and interfacial hydrogen bonds, regardless of pectin’s charge density. On the other hand, the adhesion force is increased by 1.1 times with a pectin molecule between the CNC (110) surfaces. Adhesion, however, reduces to 1/5 between CNC (200) surfaces with embedded pectin, which is attributed to disrupted$$\pi$$ $\pi$-$$\pi$$ $\pi$interaction. The simulation results reveal the atomistic level interaction between pectin and cellulose nanocrystals, which is essential for designing nanocomposites using pectin and cellulose nanocrystals as main components.