Disclosed is a method for predicting an elution order of compounds in a mixture. The method includes (a) building a quantitative structure-retention relationship (QSRR) model and (b) predicting a chromatographic elution order of the compounds in the mixture on the basis of the QSRR model using mathematical programming. The mathematical programming is a non-linear programming technique in which a predicted elution order of the compounds is used as a constraint or a multi-objective optimization (MOO) in which a retention time prediction error and an elution order prediction error are used as objective functions. With the use of the method of the present disclosure, it is possible to optimize separation of complex mixtures in reversed-phase chromatography by enabling identification of accurate positions of individual compounds that provides higher certainty in identifying a given compound, e.g., during an “omics” analysis (proteomics, metabolomics, etc.).