Polysaccharide-based nanoparticles such as pectin had always been of greatest interest because of its excellent solubility and mucoadhesive nature and are highly suitable for oral drug delivery for drug administration. In this study, we used commercially available pectin samples based on their degree of esterification, and nanoparticles were fabricated by the ionotropic gelation method using magnesium (Mg2+) as the divalent cross-linker. We conducted a comparative analysis on the three pectin NPs—high methoxylated pectin (HMP), low methoxylated pectin (LMP), and amidated LMP (AMP)—to examine the difference in characteristics such as shape, size, and biocompatibility. HMP and AMP were found to be similar in size (~850 nm), whereas LMP was found to be of ~700 nm. The three NPs were also tested for their biocompatibility toward THP-1 cells. All three NPs were found to have the potential as a nanocarrier of therapeutic and preventive drugs, especially through oral routes.