The present study investigated the structural disparities in cell wall polysaccharides between lotus rhizomes with mealy and crispy textures through a combination of acid and enzyme treatments. The results from size exclusion chromatography equipped with multi-angle light scattering detectors, viscometer detector and differential refractive index (SEC-MALS-DRI-VD) indicated that, before and after acid treatment, the CASP (alkali-soluble polysaccharides from crisp lotus rhizomes) were all semi-flexible chains using, while MASP (alkali-soluble polysaccharides from mealy lotus rhizomes) changed from flexible chains to semi-flexible. The atomic force microscope (AFM) images revealed a reduction in pectin chain length and decreased chain height of CASP following acid hydrolysis. However, MASP exhibited adhesion of pectin chains and formation of cluster structure. Through the analysis of monosaccharide composition result, the structural disparities between pectin are closely linked to the acid hydrolysis discrepancies observed in CASP and MASP. This study offers a molecular-level rationale for enhancing the thermal texture of fruits and vegetables through acid treatment.