Abstract: G-quadruplex, readily formed by the folding G-rich DNA, is supposed to have diverse of critical functions for transcriptional regulation, DNA replication and genome stability. However, restricted by insufficient sensitivity of fluorescence detection technique, a large number of G-quadruplex identification technologies are not widely used. To relief the problem, the unique spongy nanoporous disks (SNPD) was prepared and explored to establish a highly sensitive surface enhanced Raman scattering (SERS) sensor for G-quadruplexes identification, in which SNPD was used as the substrate of surface enhanced Raman scattering sensor and malachite green as the signal molecule. The SNPD has a diameter of 360 nm, a height of 75 nm and an internal pore size of 15 nm. Its unique spongy structure, abundant ligament structure and high density porous structure provided a great deal of enhanced hotspots as well as binding sites, greatly heightens the Raman vibration peak of MG signal molecule, and significantly improves the detection sensitivity of G-quadruplex, with the detection limit as low as 100 pmol / L. Besides, the G-quadruplexes could be utilized as scaffolds to capture MG molecules onto the surface of SNPD, without extra complicate labeling process. Such capture action was not found in ssDNA and dsDNA, indicating the good selectivity of the proposed SERS sensor.