Molecular characterization of nanocomposites is of great significance for the design, prediction, and understanding of the structure and properties of nanocomposites. Herein, a molecular dynamics simulation method is employed to investigate the structures, thermodynamical, and mechanical properties of carbon nanotubes (CNTs) reinforced polylactic acid (PLA) composites, as well as the effects and mechanisms of CNTs on the structure and mechanical properties of PLA matrices. The concentration profile result suggests that the type of CNTs has a significant influence on the distribution of PLA molecular chains, with relative concentration profiles around CNTs in the order of PLA/CNTs-COOH > PLA/CNTs-OH > PLA/CNTs-NH 2 > PLA/CNTs. Incorporating CNTs into the PLA matrix decreases the FFV and mobility of the polymer, where the trend is PLA > PLA/CNTs > PLA/CNTs-NH 2 > PLA/CNTs-OH > PLA/CNTs-COOH. Meanwhile, the tensile properties of the PLA matrix increase with the incorporation of CNTs, and the trend agrees with the results of fractional free volume (FFV) and relative concentration distribution. Finally, the analysis results of interaction illustrate that hydrogen bond interactions between PLA molecular chains and the functional groups on CNTs surface are involved in the adsorption of the polymers on the CNTs surface, thus affecting their interfacial interaction, structure, and properties.