Hollow silica nanoparticles (HSNPs) exhibit strong potential for industrial applications, including display coatings and nano-abrasives for semiconductor manufacturing, due to their unique optical and structural properties. This study examines how changes in ammonia concentration, acting as a catalyst during HSNP synthesis, affect structural evolution. At elevated ammonia levels, yolk–shell nanochains consisting of multiple hollow cores and internal silica nanoparticles are formed. Furthermore, HSNPs are shown to function as nanoreactors for the formation of secondary nanoparticles, as demonstrated by yolk–shell ceria@HSNP composite particles, indicating that HSNP morphology can be predictively controlled through simple concentration tuning. *This study was supported by the Technology Innovation Program (RS-2024-00415221) from the MOTIE, funded by the Korean government.