In this research, sensing performance of mono and bimetallic nanophotonics SERS sensors of gold-silver nano-columns for the detection of chlorpyrifos was investigated. For optimum substrates for Gold-silver/nano-column surface-enhanced, Raman scattering (SERS) was achieved with the silicon substrate. By combining the Ag SERS activity with the Au chemical stability and nano-columns Si large field enhancement, the Au-Ag/nano-columns Si substrate revealed perfect reproducibility, homogeneity, sensitivity in addition to chemical stability. The sensors were tested by Atomic force microscope (AFM), field emission scanning electron microscope (FESEM), energy-dispersive X-ray analysis (EDS), and X-ray diffraction (XRD). Findings presented in this research indicated modified distributions and sizes of formed alloy nanoparticles, and the hot spots junctions within the nanophotonics layer after changing the nanoparticles types. The SERS sensors performance displayed an excellent recognition of ultra-low concentrations of chlorpyrifos solutions with an exponential relationship with the Raman signal. The highest enhancement factor (Ef=1.56×106) and minimum limit of detection 0.069 mg/Kg were obtained with Au-Ag sensors.