Hydrophilic interaction liquid chromatography (HILIC), as a powerful LC method for polar compounds, has gained increasing attention in developing new HILIC stationary phases and analytical methods. Instead of using standardized substance representing different molecular force types to evaluate chromatographic performance, the analyte targets, structural analogues of matrine and oxymatrine, are applied to modulate the preparation of carboxyl group modified column in a HILIC mode. The feasibility of target-modulating preparation of HILIC column was demonstrated that target-involved optimization could effectively reflect the performance of analytes directly onto the modulation of column preparation, and hence optimize out suitable preparation conditions different from otherwise methods. And the resulting monolith was tested in the analysis of the standard medicinal materials of Sophorae flavescentis radix. The target-modulating strategy was proved to be an efficient alternative to guide the preparation of HILIC monolith column.