The development of recyclable surface enhanced Raman scattering (SERS) based sensors has been in huge demand for trace level explosives detection. A simple, hybrid Silicon (Si) nanotextured target-based SERS platform is fabricated through patterning micro square arrays (MSA) on Si using femtosecond (fs) laser ablation technique at different fluences. Using the hybrid target Si MSA substrate loaded/decorated with Ag-Au alloy NPs (obtained using femtosecond ablation in liquids) we demonstrate the trace level detection of organic nitro-explosives [picric acid (PA), 2,4-dinitrotoluene (DNT), and 1, 3, 5-trinitroperhydro-1, 3, 5-triazine (RDX)] and their mixtures. The microstructures/nanostructures of MSA fabricated at an input fluence of 9.55 J/cm2, and decorated with Ag-Au alloy NPs, exhibited exceptional SERS enhancement factors (EFs) up to ∼1010 for MB, ∼106 for PA, and ∼104 for RDX with the detection limits obtained being ∼5 pM, ∼36 nM, and ∼400 nM for MB, PA and RDX respectively. Furthermore, we demonstrate these SERS substrates possess good reproducibility (RSD values < 15%) and a superior performance compared to a commercial Ag substrate (SERSitive, Poland). Three binary mixtures, i.e. MB-PA, MB-DNT, PA-DNT at different concentrations, were also investigated using the same SERS substrate to test the efficacy. Further, the SERS spectra of dyes, explosives, and complex mixtures were utilized for discrimination/classification using principal component analysis.