Individual cells are the smallest units of the plant tissue structure, and their structure and physicochemical properties are essential for whole food processing. In this study, cassava cells were isolated using acid-alkali, hydrothermal, and pectinase methods, and the differences in microstructure and physicochemical properties among the cells, starch, and whole flour were investigated. Cassava cells isolated using pectinase showed intact individual cells with a higher isolation rate and less damage to the cell wall structure and intracellular composition. The presence of cell walls in intact individual cells inhibited the swelling and leaching of starch, resulting in a lower peak viscosity and higher gelatinization temperature than those of starch. The intact cell structure and non-starch composition enhanced the shear resistance of the gels in the sample. Heat treatment led to the gelatinization of intracellular starch and increased the permeability of the cell wall, destroying the physical barrier function of the cell wall; however, the compact cell matrix and non-starch components can inhibit starch hydrolysis. This study suggests that cells isolated using pectinase can be used to investigate the effect of cell walls on the functional properties of intracellular starch in cassava. The isolated cells provide new insights into the cassava industry.