Polymer bio-nanocomposites are widely used nowadays in various applications. One of the most promising polymers for producing such materials is poly(lactic acid) (PLA) filled with cellulose nanocrystals (CNCs). To increase the compatibility of hydrophobic PLA and hydrophilic cellulose, the surface of the latter can be chemically modified. Among the various surface modifications, the grafting of lactic acid oligomers (OLAs) is of special interest. In this paper, the first all-atom molecular dynamics simulation of nanocomposites of PLA filled with CNCs with surface-grafted OLAs is presented. The influence of the degree of modification of the CNCs with OLA chains on the PLA structure near the CNC surface and on the grafted OLA, as well as on the thermal and mechanical properties of the nanocomposites is studied. It is demonstrated that a 50% modification of CNCs with OLA chains leads to PLA expulsion from the CNC surface.