In this work, we demonstrated a facile approach for fabrication of Au nanoflowers (Au NFs) using an amino-containing organosilane, 3-aminopropyltriethoxysilane (APTES), as a shape-directing agent. In this approach, the morphology of the Au particles evolved from sphere-like to flower-like with increasing the concentration of APTES, accompanied by a red shift in the localized surface plasmon resonance peak from 520 to 685 nm. It was identified that the addition of APTES is profitable to direct the preferential growth of the (111) plane of face-centered cubic gold and promote the formation of anisotropic Au NFs. The as-prepared Au NFs, with APTES on their surface, presented effective catalytic and surface-enhanced Raman scattering (SERS) performances, as evidenced by their applications in catalyzing the dimerization of p-aminothiophenol and monitoring the reaction process via in situ SERS analysis.