Starches isolated from the bulbs of Pueraria lobata (Willd.) Ohwi (PLO) and Pueraria thomsonii Benth. (PTB) were hydrolysed by glucoamylase for different lengths of time (2, 4, 8, 12, and 24 h). The hydrolysis results were compared by scanning electron microscope (SEM), X-ray power diffractometer (XRD), and differential scanning calorimetry (DSC). The SEM results revealed that both of the PLO and PTB starches showed the same hydrolysis mechanism, which indicated that the glucoamylase primarily attacking the exterior of starch granules and then the interior. The results of XRD revealed the crystalline type of PTB starch changed from C-type to A-type with crystallinity reducing from 43.5 to 20.9% during the hydrolysis. Unlike PTB starch, the PLO starch did not show marked changes in crystalline style but lower degree of crystallinity was obtained from 32.4 to 13.7% during the hydrolysis. All the XRD results demonstrated that B-type polymorph was preferentially degraded than A-type polymorph in the C-type starch. The DSC results revealed that both of the PLO and PTB starches showed decreased enthalpy of gelatinization (ΔHgel) and gelatinization temperature range (R)-value after hydrolysis, while the gelatinization temperature (Tp) indicated different tendency, initially ranging from 68.6 to 64.3°C and then increasing to 67.8°C for PLO starch. While for PTB starch, the Tp-value showed progressive reduction from 85.4 to 74.3°C during the whole process.