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Infrared (IR) spectra were collected on a series of blends of poly(lactic acid) (PLA) and poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (P(3HB-co-3HHx) (3HHx=13.4 mol%)) using a single-bounce temperature-controlled attenuated-total-reflection (ATR) accessory with a diamond internal reflection element (IRE). Different approaches were used to analyze the raw spectral data, including peak positions, widths and intensities, principal components, and 2D correlation spectra. Differences in the interactions between the functional groups of the components become apparent as a function of temperature and composition. This study provides insights into the submolecular-level interactions and miscibility of this polymer blend system. In particular for the 40/60 PLA/P(3HB-co-3HHx) blend, two types of crystalline P(3HB-co-3HHx) CO bands were observed. The band representing a more-ordered local CO environment had a peak absorbance at a lower wavenumber than the second, less-ordered CO species. The 2D IR correlation analysis also revealed that the more-ordered material disappeared first upon heating of the sample and the amorphous P(3HB-co-3HHx) CO band formed before the less-ordered P(3HB-co-3HHx) CO band disappeared. This observation is likely the result of the less-ordered crystalline form being replenished by thermally induced disordering of the more-ordered crystalline form. Thus, the less-order crystalline material may be viewed as an intermediate form during the melting process. In the 80/20 PLA/P(3HB-co-3HHx) blend, it was observed that the lower wavenumber peak in the PLA CO doublet preferentially interacts with amorphous P(3HB-co-3HHx). When 10–20% P(3HB-co-3HHx) is added to PLA, the crystallinity of P(3HB-co-3HHx) is restricted, probably due to domain size restriction and inherent low nucleation density. These IR results suggest that P(3HB-co-3HHx) has the potential to increase the toughness of PLA dramatically, thereby enlarging the design space of sustainable materials achievable by blending.