Blending polylactic acid (PLA) with polyhydroxyalkanoates (PHAs) represents a compelling approach to achieve fully bio-based blends with favorable properties. This work employed molecular dynamics (MD) simulations to study the miscibility of PLA and PHA with different side chain functional groups. The miscibility of the blends was assessed through analyzing snapshots of the blends, pair correlation function, radius of gyration, interaction energy, solubility parameter, and Flory−Huggins interaction parameter. Results revealed that the miscibility with PLA is predominantly affected by the polarity of the side chain functional group of PHA. To achieve effective blending with PLA, it is advisable to use PHAs with non-polar side chain groups. Examination of the glass transition temperature (Tg) for the miscible blends reveals that the rigidity of PLA can be reduced by blending with PHA bearing non-polar side chain functional groups.