<p>The properties of compatibilizers in biodegradable polymer nanocomposites (PNCs) have been extensively investigated, but potential mechanisms and changing patterns of the properties of modified PNCs have not been thoroughly researched. In this study, we construct the PNCs composed of PLA/PBAT blends with either cellulose nanocrystals (CNCs) or β-cyclodextrins (CDs) as the nanoparticles (NPs), and further modify them using one of the following combinations of compatibilizers: chain extender ADR4468 or silane coupling agents (SCAs) KH550 or KH560, then testing the performance of the obtained PNCs. At the same time, fully atomistic molecular dynamics simulations (FAMDs) were employed to investigate the influence of these additives at different loading concentration in the PNCs. Herein, we characterized the mechanical, thermal and compatibility behaviors with both experiments and simulations. The results reveal that at high addition amounts of NPs, different types of compatibilizers have different performance effects on the PNCs. That is to say, different compatibilizers exert distinct effects on PNCs: ADR4468 significantly regulates the thermal transition and promotes the compost biodegradation of PNCs. Furthermore, SCAs mainly improve the interfacial compatibility between matrices and NPs with little influence on the rheological properties of PNCs. Because of the structural differences, CNCs and CDs show different modification responses to compatibilizers, and each compatibilizer has an optimal amount for performance enhancement. The simulation results are highly consistent with the experimental trends of mechanical strength,<i> T</i>_g and compatibility. The modification effects of three compatibilizers at different dosages on PNCs were systematically studied through our studies, and the results of experiments and simulations mutually confirm each other, providing practical methods for the screening and prediction of material formulations.</p> Graphical abstract <p></p>