The　protein　nanoenvironment　on　the　plasma　membrane　is　intimately　linked　to　cellular　biological　functions.　Elucidation　of　the　protein　nanoenvironment　contributes　to　understanding　the　pathological　mechanism　and　discovery　of　disease　biomarkers.　However,　methods　enabling　characterization　of　the　protein　nanoenvironment　in　the　endogenous　biological　environment　have　been　rarely　developed.　Toward　this　end,　we　created　a　nucleic　acid　tool　called　Apt-Gq/h　for　proximity　labeling　to　decipher　the　endogenous　protein　nanoenvironment.　Here,　the　aptamer　acts　as　an　anchor　for　binding　the　protein　of　interest　(POI).　The　G-quadruplex/hemin　complex　induces　proximity　labeling　of　POI　via　catalyzing　the　conversion　of　inert　small-molecule　substrates　into　short-lived　reactive　species.　The　labeled　proteins　enable　the　subsequent　affinity-based　enrichment　and　proteomic　analysis.　We　first　characterized　Apt-Gq/h-mediated　POI　labeling　in　vitro　and　tested　its　utility　by　interrogating　the　protein　nanoenvironment　of　POI　in　living　cells.　Taking　advantage　of　the　nongenetic,　multiple　reaction　sites,　and　rapid　proximity　labeling,　Apt-Gq/h　was　further　utilized　to　imaging　the　cell–cell　connection　and　amplification　detection　of　biomarkers　in　living　cells　and　tissue　sections.　We　believe　that　Apt-Gq/h　will　be　a　potential　tool　for　basic　science　and　clinical　applications.　©　2021　American　Chemical　Society