The effects of molar ratio and carboxylic acids' structure of deep eutectic solvents (DESs) on the treatment of waxy maize starch (WMS) were systematically investigated. FT-IR results of DESs discovered that shorter carbon chain acids exhibited stronger hydrogen bonds. Subsequently, DESs were utilized to treat WMS. Microscopy, DSC, and viscosity measurements indicated that the dissolution and gelatinization phase transitions of WMS occurred simultaneously in acid-DESs. Specifically, shorter carbon chains led to lower viscosity and more obvious dissolution. Notably, relatively high solubilities of 57.02 wt% (choline chloride/formic acid, CF) and 53.39 wt% (choline chloride/oxalic acid dihydrate, CO) were obtained for 6 h at 60 °C. Further characterization of regenerated WMS using SEM, XRD, FT-IR, and GPC showed that the granular and crystalline structures of WMS were disrupted, with a significant decrease in molecular weight. The extent of starch disruption/degradation increased as the acids' carbon chain decreased. Therefore, the treatment of WMS in acid-DESs was predominantly influenced by the length of the acids' carbon chain. Additionally, esterification reactions between WMS and carboxylic acids were detected in the CF and CO systems. These findings could provide a promising and efficient approach for starch treatment and structural analysis.