Amino-functionalized silica has attracted a great deal of interest due to its high surface reactivity and potential for diverse applications across various fields. While the classical co-condensation method is commonly used to synthesize aminofunctionalized silica particles, the mechanism of the reaction between (3-aminopropyl)triethoxysilane (APTES) and tetraethoxysilane under different conditions remains unclear, leading to unexpected self-nucleation or cross-linking between silica particles and consequently hindering rational control over the extent of functionalization. To address this issue, we systematically explored the co-condensation growth mechanism of amino-functionalized silica particles in the Stober method by investigating the effects of APTES concentration and water content on the hydrolysis and condensation of silanes. The experimental results revealed that APTES could decrease the rate of hydrolysis/condensation, while the moderate water content promoted both the rate of hydrolysis/condensation and the overall quality of the silica particles. Consequently, we successfully demonstrated the rational synthesis of amino-functionalized silica particles with diameters ranging from 213 to 670 nm and a nitrogen content of ≤2.8 wt %. The relationship between the APTES concentration and particle properties exhibited a biphasic trend. At low APTES concentrations (≤2.0 mM), the particle size remained stable while the isoelectric point increased rapidly. Further increasing the APTES concentration from 2.0 to 100.0 mM induced a decrease in particle size due to APTES's inhibitory effect on silica growth, with nitrogen content continuing to increase even after the isoelectric point remained unchanged. These silica particles, featuring varying surface amino group densities, were utilized as matrices for loading Au nanoparticles. The resulting functionalized particles exhibited distinctive catalytic ability in the reduction of 4-nitroaniline, demonstrating significant potential for applications across various fields.