A novel stationary phase co-modified with N-isopropyl acrylamide (NIPAM) and 3-aminophenylboronic acid copolymer on the silica was synthesized through atom transfer radical polymerization (ATRP) reaction for performing mixed-mode and boronate affinity chromatography. The prepared functionalized silica was characterized using Fourier transform infrared spectrometry (FT-IR), elemental analysis (EA) and thermogravimetric analysis (TGA), scanning electron micrographs (SEM) and Brunauer-Emmett-Teller (BET) measurements. The prepared column named Sil-PBA-NIPAM showed great separation performance for hydrophobic, hydrophilic, positional isomer, acidic and alkaline compounds. Besides, the mixture of cis-diol and non-cis-diol compounds was used to prove that the developed column also has potential to capture and enrich cis-diol compounds. The prepared column possesses merits of time-saving, high selectivity to cis-diol compounds and molecular-planarity selectivity compared with two commercial single-mode columns. The theoretical plates of material can reach to 57472 and the column has good hydrolysis stability and batch-to-batch reproducibility. In summary, the prepared column possesses good hydrophilicity, hydrophobicity, molecular-planarity selectivity and boronate affinity abilities for the analysis of various compounds.