This study investigates the utilization of choline hydroxide as a cocatalyst in the Stober method to synthesize silica particles with controlled microstructure. Under low ammonia concentration, we add a robust organic base choline hydroxide and systematically explore the influence of choline hydroxide concentration on the hydrolysis and condensation equilibrium of tetraethyl orthosilicate (TEOS). Through the rational control of the water content, we significantly enhance both the size range and polydispersity of the resulting silica particles. Taking advantage of the regulated microstructure induced by controlled hydrolysis and condensation catalyzed by choline hydroxide, we achieved silica particles with hollow structures through hot water etching, exhibiting significantly enhanced surface area. These findings demonstrate the versatility of choline hydroxide as a cocatalyst in tailoring the microstructure of silica particles. In addition, due to its reducing ability and biocompatibility, which are not shared by other reported catalysts, the use of choline hydroxide opens up opportunities for applications in catalysis, sensing, and drug delivery.