Surface-enhanced　Raman　scattering　(SERS)　is　a　promising　technique　for　detecting　trace　analytes,　but　the　design　of　hotspots　with　nanoscale　precision　remains　a　challenge　for　achieving　accurate　detection.　Here,　photoinduced-synthesized　single-atom　sites　Ag　are　uniformly　dispersed　on　an　Au　nanostructure　to　form　hierarchical　hotspots.　The　precise　control　of　hotspots　exhibits　significantly　improved　SERS　performance　with　an　enhancement　factor　(EF)　of　more　than　109　and　great　Raman　signal　quantification　for　pesticide　residue　acetamiprid　and　cycocel.　The　superiority　of　the　precise　structure　of　hierarchical　hotspots　can　be　ascribed　to　structure　uniformity　and　enhanced　electronegativity,　leading　to　a　limit　of　detection　(LOD)　of　down　to　0.1　ppb　and　notable　improvement　of　Raman　signals　stability　compared　with　bare　Au　nanostructure.　The　LOD　is　among　the　best　SERS　substrates　in　literatures.　Furthermore,　the　precise　hotspot　modification　approach　can　be　identified　immediately　by　coloration　under　sunlight　and　applied　to　a　SiO2　substrate　to　avoid　the　Ag　oxidation　in　ambient　conditions.　Thus,　the　simple　and　effective　SERS　enhancement　method　via　single-atom　site　decoration　strategy　is　anticipated　to　shed　light　on　practical　sensing　detection.