Lignin is widely recognized as a key factor influencing the recalcitrance of lignocellulosic biomass, yet the specifics of this relationship remain complex and not fully understood due to the complex interplay between lignin content variation and cell wall structure. Bamboo, which exhibits greater recalcitrance compared to wood in biorefinery processing, was chosen as the focus of investigation in this study. Three variants of Dendrocalamus farinosus with high, middle and low lignin contents were systematically analyzed and compared, in terms of molecular structure of lignin, hemicelluloses and cellulose, cell wall polymer spatial orientation, lignin-carbohydrate complex (LCC) linkages, cell wall geometrical size, as well as deconstruction efficiency, including delignification, alkaline extraction, and cellulose enzymatic hydrolysis efficiency. Findings reveal that an increase in lignin content generally lowers bamboo's deconstruction efficiency, but the mechanisms are more nuanced than previously thought. While lignin content variations do not significantly affect the molecular structure of xylan, cellulose and the chemical linkage type of LCC linkages, they do impact cellulose crystallinity, xylan orientation and notably, the thickness of fiber cell wall in the free fiber stands of bamboo. These findings highlight that lignin's role extends beyond mere physical protection of the cell wall, but also induces subtle variations in polymer structure and cell wall morphologies, which collectively influence the deconstruction efficiency of bamboo cell walls.