With the increasing demands for medical diagnosis, more and more attention has been paid to the technology of biomolecular detection. As a high throughput and multiplexed molecular detection method, suspension array has developed rapidly in recent years. In this study, a Raman spectra-encoded suspension array with micro-quartz pieces as the carrier was prepared by the layer-by-layer self-assembly method, and a high sensitivity and high resolution optical system was built to realize the qualitative and quantitative analysis of the suspension array. The home-built optical system was obtained by coupling Raman spectroscope with a fluorescence microscope. For the Raman spectroscope, a 785 nm laser was converged on the sample through dichroic mirrors, reflector and object lens. Then the Raman scattering light produced by the sample passed through the objective lens, anti-reflection mirror, dichroic mirror and Raman filter, and focused on the slit of the spectrometer via the concave lens. And finally, Raman spectra can be obtained by the dispersion effect of the spectrometer. For the fluorescence microscope, which used the optical imaging principle, the excitation light could irradiate the sample uniformly through the objective lens by adjusting the distance between the concave lens and the excited light of 405 nm. Then, the emitted fluorescence passed through an objective lens, an anti-reflection mirror, dichroic mirror, a filter and a concave lens, and finally imaged on the matrix CCD. The coupling of the Raman spectroscope and the fluorescence microscope was completed by improving the optical path of the conventional portable Raman spectroscope and selecting the anti-reflecting mirror with the specific band and the objective lens with a focal length of 20×. In order to reduce the interaction between the Raman spectroscope and the fluorescence microscope, the appropriate dichroic mirror and filter were selected to improve the coupling system. The Raman spectra of the suspension array were detected by home-built system to accomplish the qualitative identification of each encoded micro-quartz pieces. At the same time, the fluorescence of the encoded micro-quartz pieces was excited and the fluorescence signal was collected to complete the quantitative analysis of the target analyst according to the fluorescence intensity value on each encoded micro-quartz pieces. Compared with traditional fluorescence-encoded suspension arrays, Raman spectra encoding method has the advantages of stronger stability and higher spectral resolution. This optical system integrates Raman spectroscope and fluorescence microscope, which solves the problem that there is no suspension array detection system based on Raman encoding method at present and can qualitatively and quantitatively analyze a variety of target molecules at the same time, improving the accuracy of the experimental results.