The cell walls of parenchyma cells and fibers in bamboo are both highly lignified with secondary thickening. However, the former were found to have much higher nanofibrillation efficiency than fibers via both protocols of ultrasonication and high pressure homogenization. To elucidate the inherent mechanism, detailed comparisons of chemical composition, cell morphology, cell wall density, pore structures, and structural organization of cell wall polymers were performed on native and pretreated cell walls of both parenchyma cells and fibers. Chemical compositional analysis showed that fibers have much higher cellulose (49.8% to 35.5%) but lower xylan content (21.1% to 36.2%) than parenchyma, while their lignin contents were similar (24.9% vs 22.9%). Polarized FTIR further revealed clear differences in the structural organization of polymers between the two types of cells, with all the polymers of fibers being more orderly assembled than those of parenchyma cells. The compact arrangement of polymers in the fibers was also supported by the much higher cell wall density (1.52 vs 1.28 g/cm3) and lower porosity (0.007 vs 0.013 cc/g after chemical pretreatments), as compared to the parenchyma cells. The study provides evidence that the anatomical characteristics of huge cavity-wall ratio, higher cell wall porosity, and less ordered arrangement of cell wall matrix polymers (mainly lignin) in parenchyma cells contribute to their higher nanofibrillation efficiency compared to fibers.