Poly(lactic acid) (PLA) has its own limitations in terms of slow crystallization rate and low crystallinity during processing, resulting in poor toughness and thermal stability, which seriously restricts the practical application of PLA. Blending nanoparticles into the PLA matrix is an effective way to improve PLA crystallization. In this study, carbon dots (CDs) were prepared by green oxidation using weathered coal as carbon source and then surface-modified with dodecylamine (DDA) and octadecylamine (ODA). Modified CDs (MCDs)/PLA composite films were prepared using MCDs as filler to improve the crystallinity and toughness of PLA films. The results showed that the improvement effect of ODA-modified CDs (ODACDs) was better than that of DDA-modified CDs (DDACDs). The crystallinity of PLA composite film (0.05 wt% ODACDs) was increased from 7.20% (pure PLA film) to 35.44%, and its elongation at break was increased by 5.01 times compared with that of the pure PLA film. Moreover, thermogravimetric analysis suggested that the thermal stability of MCDs/PLA films was also improved. The results of simultaneous rheology and in-situ FTIR analysis as well as molecular dynamics simulations confirmed that MCDs had a strong interaction with PLA molecules, which promoted the crystallization of PLA film, thereby improving its toughness and thermal stability.