Synchronous fluorescence spectroscopy (SFS) coupled with two-dimensional correlation spectroscopy (2DCOS) was employed to monitor, at the molecular level, the coagulation of five mixture ratios of camel’s milk (CaM) and cow’s milk (CM) (100% CaM, 75% CaM:25% CM, 50% CaM:50% CM, 25% CaM:75% CM and 100% CM). The dissimilarities among the different formulations are highlighted on the synchronous 2DCOS-SFS. In addition, according to the cross-peak symbols in synchronous and asynchronous spectra, the rate of response modification in riboflavin, protein and vitamin A matched with common coagulation phenomena usually reported during chymosin coagulation (hydrolysis of κ-casein, destabilization of casein micelles and aggregation). This study demonstrated that 2DCOS-SFS is a successful strategy to discriminate milk mixtures and to monitor molecular structure modifications during coagulation process.