For revealing the degradation effect of acid-alcohol modification on starch, commercial com and potato starches were hydrolyzed by 0.36% HCl in methanol at 25°C for 1 to 15 days. Results showed the yields of the modified starches ranged from 91 to 100%, and the average granule size of the modified starch was slightly smaller as compared to their counterpart native starches. After 15 days of modification, no significant configuration change was found whereas the solubility of starches obviously increased with the increase in the hydrolysis time. Com starch showed a slower increasing tendency than that of potato starch. Gelatinization onset temperatures (To) of starches after modification showed a decrease tendency in com starch, and an increase tendency in potato starch. For both com and potato starches, the peak (Tp) and conclusion (Tc) temperatures of gelatinization increased with the increase in the treatment time. Consequently, the range of gelatinization increased from 12.2 to 23.9°C for com starch, and from 12.8 to 19.8°C for potato starch. However, the gelatinization enthalpies (•H) of modified starches showed 1 to 2 J/g lower than their counterpart native starches. For the acid-alcohol treated starches, the area of amylopectin fractions determined by high-performance size exclusion chromatography (HPSEC) decreased with the treatment time. Compared to the gradual degradation pattern of com starch, potato starch showed a stepwise pattern. The weight average degree of polymerization (DPw) of starches rapidly decreased within the first 5 days of treatment, and potato starch had a higher rate of decrease than com starch. The number average degree of polymerization (DPn) of com and potato starches after acid-alcohol treated for 15 days were 162 and 183, respectively. It was concluded that the degradation of amylopectin by the acid-alcohol modification might alter the molecular structure of starch, which resulted in the fast disruption of granule and the decrease of viscosity of starch paste during heating.