Substantial knowledge gap still exists in understanding Stöber silica’s confusing microporosity. In this work, we utilized simultaneous thermal analysis coupled with Fourier transform infrared spectroscopy to characterize Stöber silica samples prepared with various post-treatments including water or ethanol washing and drying at different temperatures. The results suggest that ammonia-catalyzed ethoxylation between ethanol and silanol groups can take place during drying, and the resulting ethoxyl groups along with Si-containing oligomers may contribute to serious micropore blocking. On the other hand, water washing is effective to hydrolyze and remove these pore-blocking materials and thus enable cleared micropores. Several interesting findings including the very sharp DSC peaks, high evolving temperature of ethanol, and pyrolysis of organic matters are linked to Stöber silica’s micropores. Our work has undoubtedly improved the mechanistic understanding of Stöber silica’s microporosity and will thus facilitate the practical optimization and application of this material.