In order to increase agricultural productivity, several countries heavily rely on deadly insecticides, known to be toxic to most living organisms and thus significantly affect the food chain. The most obvious impact is to human beings who come into contact, or even consume, pesticide-exposed crops. This work hence focused on an alternative method for insecticide detection at trace concentration under field tests. We proposed a compact Raman spectroscopy system, which consisted of a portable Raman spectroscope, and a surface-enhanced Raman scattering (SERS) substrate, developed for the purpose of such application, on a chip. For the selected portable Raman spectroscope, a laser diode of 785 nm for excitation and a thermoelectric-cooled CCD spectrometer for detection were used. The affordable SERS substrates, with a structure of distributed silver nanorods, were however fabricated by a low-energy magnetron sputtering system. Based on an oblique-angle deposition technique, several deposition parameters, which include a deposition angle, an operating pressure and a substrate rotation, were investigated for their immediate effects on the formation of the nanorods. Trace concentration of organophosphorous chemical agents, including methyl parathion, chlorpyrifos, and malathion, adsorbed on the fabricated SERS substrates were analyzed. The obtained results indicated a sensitive detection for the trace organic analyses of the toxic chemical agents from the purposed portable SERS system.