This study investigated the effect of phase transformation on indomethacin (IMC), cimetidine (CIM), and their 1:1 eutectic mixture, using FTIR spectra and multivariate analysis. The IMC form γ, CIM form A, and IMC-CIM 1:1 mixture molar ratio samples were heated on a hot plate at 303–453 K for 5 min and cooled till room temperature. The prepared samples were investigated by powder X-ray diffraction analysis and infrared spectroscopy with KBr powder. The PXRD patterns suggested the bulk IMC form γ, bulk CIM form A, and 1:1 physical mixture samples phase transformed into low-crystallinity IMC form γ, amorphous CIM, and eutectic mixture, respectively. FTIR spectra combined with singular value decomposition (SVD) suggested by absorbance peak shifts of several vibration modes that the polymorphic transformations of the samples affect their molecular interactions. The estimated melting points of heated samples were evaluated by sigmoid fitting based on the SVD results. The principal components of SVD show that the process of phase transformation of IMC-CIM 1:1 mixture samples affect the IR vibration of the C[dbnd]O stretch of IMC and the C-C stretch and C-H bending of CIM. These results suggest that molecular interaction is an important factor in the eutectic condition of IMC-CIM 1:1 mixture. This observation enables to evaluate for in co-amorphous formulations or stability of drug combinations in a poly pill.