The processability and practical applications of poly (butylene adipate-co-terephthalate) (PBAT) /poly (lactic acid) (PLA) blends are limited due to their lower miscibility. To investigate the miscibility of various PBAT/PLA composite ratios and the mechanism of miscibility between them, PBAT/PLA blends with different ratios were prepared using the melt mixing method. A combination of multi-scale simulations and experiments were employed to investigate the miscibility of the composites. Molecular dynamics simulations analyzed PBAT/PLA mixtures that are incompatible and showed the molecular basis of their incompatibility through the radial distribution function (RDF). The degree of miscibility of different ratios of PBAT/PLA composites was described using the Flory–Huggins interaction parameter, indicating that the 50/50 PBAT/PLA blend has the worst miscibility. Mesoscopic dynamics described the mesoscopic morphology of PBAT and PLA blends visually. The results obtained from the simulations were consistent with scanning electron microscope (SEM) and differential scanning calorimeter (DSC) experiments, indicating the simulations' reliability. This work provides a molecular perspective on the mechanism of thermodynamic insolubility of PBAT and PLA, which can inspire future PBAT/PLA hybrid modifications.