Genetic monitoring of disease-causing virus for point-of-care molecular diagnostics requires gene identification by nucleic acid amplification using polymerase chain reaction (PCR), with gene quantification based on fluorescence in real time. However, fluorescence-based DNA assays have some limitations for point-of-care including high potential for sample contamination and high threshold cycle number. Recently, surface-enhanced Raman spectroscopy (SERS) allows genetic quantification during PCR with high sensitivity and selectivity. However, high cycle threshold and process time remains a problem to apply for point-of-care. This work propose a new and ultrafast DNA assays for SERS-based quantitative PCR using plasmonic nanopillar arrays. The glass nanopillar arrays with gold nanoislands exhibit hight light absorption to geneate heat by photothermal effect, and strong local field enhancement as a SERS substrate. The amplification and quantification of target DNAs have been experimentally demosntrated on photothermal PCR chip. This method allows ultrafst monitoring of target gene for 20 cycle within 10 min with low cycle threshold and also offers steppint stones for highly sensitive point-of-care molecular diagnostics.