The structure and properties of bio-based polyamide 69 after subjecting to water treat at room temperature and under superheated (140 °C–280 °C) condition were studied in order to get effective information about processing and treatment of polyamides in water. They were characterized by differential scanning calorimetry, small-angle x-ray scattering, Fourier transform infrared spectroscopy, and wide-angle x-ray diffraction. Water treated at room temperature exerted a swelling effect on polyamide 69, and led to a transition in the crystallization of polyamide 69 from amorphous to α crystalline form. Polyamide 69 was dissolved in superheated water at 170 °C, and at a temperature lower than the above it led to an annealing effect, resulting in an increase in the lamellar thickness, melting temperature, and crystallinity. Besides, the dominant crystal structure was transformed from γ to α crystalline form. Above 170 °C, polyamide 69 was dissolved completely, and hydrolytic degradation was more prominent especially above 240 °C, which led to the dominant γ crystalline form was severely damaged and the amide bonds of polyamide 69 cleaved gradually to produce oligomers. Therefore, this investigation can provide potential applications information on plasticization and hydrothermal annealing treatment, low temperature melting extrusion processing, and hydrolysis and recycling of polyamides.