A novel imidazolium-embedded N,N-dimethylaminopropyl-functionalized silica-based stationary phase (Sil-ImCl) was prepared and further used for hydrophilic interaction/reversed-phase mixed-mode chromatography. The Sil-ImCl stationary phase was respectively characterized by Fourier transform infrared spectrometry, thermogravimetric analysis, and element analysis. A variety of hydrophilic or hydrophobic compounds were used to evaluate the retention mechanisms of the developed stationary phase, and the effects of buffer salt concentration and pH of mobile phase on the retention of these compounds were also investigated. The developed stationary phase was successfully applied for separation of nucleosides and nucleic acid bases, water-soluble vitamins, phenols, and positional isomers. Moreover, simultaneous separation of polar and nonpolar compounds was also achieved with high resolution, outperforming the commercially available C8 column and amino column. Furthermore, the Sil-ImCl stationary phase has been successfully applied for separation of secondary metabolites of Hansfordia sinuosae. All these results demonstrate that the Sil-ImCl stationary phase might be promising for separation of complex polar and nonpolar compounds with high efficiency, especially in biological industry.