Bio-based polyester polyols were synthesized via the polycondensation of adipic acid with different butanediol (BDO) isomers (1,4-, 1,3-, and 2,3-BDO) to investigate the effects of diol molecular structure on reaction behavior and thermal properties. The BDO isomers differ in hydroxyl position and steric environment, which influence esterification kinetics and chain growth. All reactions were conducted under identical thermal conditions to allow direct comparison. Polyol characteristics were evaluated using acid number, hydroxyl number, viscosity, gel permeation chromatography, and FT-IR spectroscopy. Thermal transitions were analyzed by differential scanning calorimetry, while thermogravimetric analysis was employed to assess thermal stability and degradation behavior. The results indicate that polyols derived from 1,4-BDO exhibit faster esterification and higher molecular weight development, whereas those based on 1,3- and 2,3-BDO show reduced reactivity due to steric hindrance and secondary hydroxyl effects. This study provides fundamental insights into the relationship between molecular structure and reactivity, enabling the design of bio-based polyester polyols with tunable properties.