A hydrophobically associating polyacrylamide (HAPM)-coated silica packing (HAPM@silica) as a novel stationary phase was synthesized by a simple thermal immobilization to separate multiple polar compounds for the first time. The successful immobilization of HAPM on the silica support was confirmed by elemental analysis, scanning electron microscopy (SEM) and the Brunauer–Emmett–Teller (BET). The thickness of HAPM coating is crucial and the one-layer HAPM@silica stationary phase was demonstrated the highest separation efficiency. Compared with the bare silica and amino modified silica, the new stationary phase showed better separation performance for multiple polar compounds such as bases, alkaloids, carbohydrates and amino acid compounds under the experimental conditions. The chromatographic behaviors were evaluated by investigating the effects of acetonitrile content, water content, mobile phase pH on separation. A typical hydrophilic interaction liquid chromatography (HILIC) retention feature of HAPM based column was observed at the low percentage of water content. The packing material also showed excellent chromatographic repeatability with intraday RSDs of the retention time of five bases less than 0.46 % (n = 10) and interday RSDs less than 1.45% (n = 5). In summary, the new chromatographic material can be used for a feasible option for analysis of polar compounds.