The　construction　of　plasmonic　nanostructures　is　a　frontier　research　area　in　the　field　of　Surface　enhanced　Raman　scattering　(SERS).　Three-dimensional　(3D)　porous　materials　coupled　with　aptamers　have　attracted　increasing　attention　for　application　in　SERS　sensing,　owing　to　their　great　promise　towards　offering　both　high　specific　and　ultrasensitive　detection　capacity.　However,　most　of　these　SERS　sensors　are　plane-shaped　or　solution-based,　which　makes　target　molecules　with　a　reduced　mass　transfer,　thus　leading　to　a　relatively　poor　capture　efficiency.　Herein,　we　demonstrate　a　capillary-based　porous　nanostructure　coupled　with　aptamers　that　can　serve　as　a　type　of　SERS　aptasensor　for　rapid　trace　detection.　The　aptasensor　was　prepared　by　immobilization　of　aptamer-modified　SERS　nanotags　on　a　porous　silica　monolith　which　was　obtained　by　an　in-situ　polymerization　in　a　capillary　with　a　facile　fabrication　process.　The　3D　porous　silica　monolith　(3D-PSM)　with　a　hierarchical　biporous　structure　that　could　enable　the　rapid　permeation　of　the　aqueous　phase　and　provide　high　specific　surface　area　and　active　sites,　endows　the　material　with　high　capture　efficiency　of　target　molecules.　Besides,　according　to　the　size　of　aptamers,　stable　and　uniformed　hotspots　of　7–8　nm　in　size　were　formed,　which　precisely　guaranteed　the　sensitivity,　specificity,　and　stability　of　detection.　The　experimental　verification　showed　that　the　proposed　aptasensor　could　detect　the　presence　of　microcystin-LR　at　concentrations　as　low　as　0.01　nmol/L,　with　fast　recognition　time　(10　min),　low　sample　consumption　(20　μL),　and　simple　operation.　All　the　results　suggest　that　this　new　strategy　has　promising　potential　in　rapid　microvolume　trace　analysis　in　various　fields.　©　2022