In this study, spherical silica with pore size varied from 30 to 200 Å was synthesized by pseudomorphic transformation at atmospheric pressure. 40–80 Å silica particles with a narrow pore distribution were obtained by using quaternary amine cationic surfactants and different kinds of swelling agents, including polypropylene glycol, 1,3,5‐trimethylbenzene, alkanes, and alkanols. Alkyl imidazolium ionic liquid surfactants were used to synthesize large pore size distribution silica spheres with pore sizes in the range of 110–200 Å. All these silica particles can be synthesized under mild conditions within 12 h, which provides a facile synthesis method for the preparation of a chromatographic matrix with tunable pore size. The method is reproducible and the relative standard deviation of silica sphere pore structure parameters in scaled‐up preparations is less than 6%. The pore size on the fraction of low‐molecular‐weight heparin (LMWH) was investigated in size exclusion chromatography. Matrixes with different pore size distributions have various size exclusion regions. By using UPS‐60‐Diol columns in a twin‐column recirculation separation process, LMWH with >85% heparin with molecular weight within the range of 3000–8000 Da were separated in five‐column volumes.