The structure and properties of bio-based polyamide 109 (PA109) after treatment with superheated water (140 ∘ C ≤ T ≤ 280 ∘ C) were investigated and characterized by Fourier transform infrared spectroscopy, differential scanning calorimetry, wide-angle X-ray diffraction, scanning electron microscopy and small-angle X-ray scattering. Below 170 ∘ C, the hydrothermal treatment was considered to be a physical process, which exerted an annealing effect on PA109. It led to an increase in melting temperature, lamellar thickness and crystallinity, while the macromolecular structure, crystal structure and the order of crystalline regions were not affected. Above 170 ∘ C, complete melting/dissolution of PA109 occurred with partial hydrolysis. Due to the high temperature and long reaction time, the hydrolysis reaction became more and more prominent, and the resin was completely hydrolyzed into oligomers at 280 ∘ C. Also, above 170 ∘ C, the hydrothermal treatment was accompanied by a chemical process and the melting temperature and molecular weight decreased progressively. Notably, the crystal structure was not altered, but the degree of perfection of crystals and the order of crystalline regions were broken, especially above 200 ∘ C. The hydrolytic degradation reaction was significantly affected by temperature, while both time and the water to polyamide ratio were secondary factors which influenced it to a minor extent. The process could be considered as a typical nucleophilic substitution reaction which takes place step by step inducing the molecular weight to decrease gradually. Overall, this study provides a 'green' route for the processing, recycling and treatment of environmentally friendly polyamides based on hydrothermal treatment technology.