Constructing　advanced　substrates　with　excellent　features　is　promising　for　sensitive　surface-enhanced　Raman　spectroscopy　(SERS)　detection.　Here　a　novel　capillary　monolithic　3D　structural-substrate　SERS　platform　with　Au@cDNA@Ag@Cyanine　3-aptamer　nanoparticles　(Au@cDNA@Ag@Cy3-Apt　NPs)　was　fabricated　for　rapid,　highly　specific　profiling　of　ultra-trace　Bisphenol　A　(BPA).　The　proposed　SERS　platform　combined　both　in　capillary　SERS　and　aptamer-affinity　recognition　strategies,　in　which　the　superior　SERS　properties　of　Au-Ag　NPs,　aptamer　selectivity,　and　the　advantages　of　capillary　monolith　were　integrated.　A　3D　hierarchically　porous　network　was　constructed　in　the　monolithic　column,　which　was　endowed　with　rich　hotspots　for　SERS,　rapid　sample　permeation,　and　better　analysis　efficiency　than　most　plane-shaped　SERS　modes.　By　varying　the　amount　of　Ag+　precursor,　the　Ag-shell　thickness　on　SERS　was　finely　tuned　to　guarantee　Cy3　label　in　proximity　to　the　plasmonic　surface.　Based　on　the　biorecognition　of　aptamer,　the　selective　identification　of　BPA　occurred　and　exhibited　a　significant　change　in　SERS　intensity　without　obvious　interference.　As　a　result,　the　monolithic　SERS　platform　featured　facile　operation,　excellent　specificity,　and　rapid　analysis　(10　min,　much　less　than　the　solution　based　or　planar　substrate　SERS　modes).　Ultra-high　sensitivity　and　robust　reproducibility　for　BPA　analysis　was　achieved　with　a　low　limit　of　detection　(LOD)　at　9.12　x　10-4　ng/L.　The　feasibility　of　this　SERS　platform　for　monitoring　BPA　in　water　and　milk　samples　was　also　validated.　This　work　lights　a　new　access　to　capillary　monolithic　SERS-sensing　platform　for　ultrasensitive　and　specific　analysis　of　BPA.