We investigated the thermal behavior of spin-coated films of biodegradable poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (P(HB-co-HHx)) copolymers at the molecular level. To better understand details of thermal behavior of spin-coated films of P(HB-co-HHx) copolymers, we applied two-dimensional (2D) correlation analysis to the spectra of P(HB-co-HHx) (HHx = 12.0, 10.0, and 3.8 mol %) copolymers during the heating process from 30 to 150 degrees C as obtained by temperature-dependent infrared-reflection absorption spectroscopy and X-ray photoelectron spectroscopy (XPS). 2D IR and 2D XPS correlation spectra of spin-coated films of P(HB-co-HHx) copolymers clearly revealed the sequence of intensity changes with increasing temperature: an amorphous band increases first and then a band for less ordered secondary crystals decreases before a band for well-ordered primary crystals. Furthermore, the synchronous 2D heterospectral XPS/IR correlation spectrum elucidated the correlation between the IR and XPS bands, confirming their band assignments. The asynchronous 2D heterospectral correlation spectrum revealed the probe-dependent asynchronicity between XPS and IR signals arising from the same species even under identical perturbation conditions because of the different scales of molecular changes probed. It clearly provides a complete interpretation of the phase transition phenomenon of P(HB-co-HHx) copolymers, which could not have been obtained through XPS or IR study alone, and also, the results obtained thereof offer a new insight into the molecular interactions as well observed by two different probes.