Abstract The properties and compatibility of bio-based PA56 and polyethylene terephthalate (PET) polymers were studied in detail. The experimental results showed that when compared with PET, bio-based PA56 had better moisture absorption, softness, and dyeing characteristics. By calculating and analyzing the macromolecular structures of bio-based PA56 and PET, the difference in solubility was obtained as 4.18 Cal0.5·cm1.5·mol−1. Thermodynamic analysis showed that the measured change in mixing enthalpy far exceeds the range of the compatible system when the proportion of bio-based PA56 exceeded 15%. When the content of bio-based PA56 in PET exceeded 20%, the glass transition temperature of the blends with different proportions all had double peaks and the eutectic phenomenon was not observed. Scanning electron microscopy was used to observe the cross-section morphology of bio-based PA56/PET blends before and after etching. We found that the interface between the two phases was clear and a “sea-island” dispersed structure was formed. The results of the analysis indicated that the compatibility of the bio-based PA56 and PET was not good.