The aim of the present study is to evaluate the potential of mid-infrared spectroscopy in combination with two-dimensional correlation spectroscopy (2DCOS) and partial least squares discriminant analysis (PLS-DA) to monitor molecular structure evolution of milk mixtures of two species (cow and camel) during enzymatic coagulation. Molecular structure changes and texture characteristics were investigated on five different milk formulations by mixing camel milk (CaM) and cow milk (CM) (i.e., CaM, CaM3:CM1, CaM1:CM1, CaM1:CM3, and CM, (v/v)). Regarding MIR spectroscopy, two spectral regions were considered to monitor milk coagulation, the fatty acid acyl-chain region (3000–2800 cm−1) and the protein region (1700–1500 cm−1). Different formulation dissimilarities were revealed through the synchronous 2DCOS spectra and their respective auto-peaks. Moreover, using the cross-peak symbols of the synchronous and asynchronous spectra helps to establish the sequence of molecular structure modifications during coagulation. Finally, the analysis of the 2DCOS-MIR synchronous and asynchronous maps by PLS-DA gave good discriminant accuracy (88 to 100%) between each formulation. Those results highlighted that different synchronous and asynchronous chemical phenomena occurred during milk coagulation depending on the milk formulation. Texture attributes were influenced by camel milk ratio in mixtures based on the initial composition of milks. Samples containing more than 50% of CM showed significantly higher hardness compared to pure CaM and CaM3:CM; however, CM gel displayed lower springiness contrary to CaM. Textural characteristics of the resulted gels also confirmed that 2DCOS MIR observations are consistent with textural observations of the gels obtained after milk mixtures coagulation.