Abstract: Based on the flow fluorescence technology and the coded microspheres decoding analysis technology of high throughput suspension chip, an optical system of flow dot matrix instrument is studied. The instrument adopts an innovative optical system design. In the laser spot shaping optical path, the secondary shaping lens multiplexing design is adopted to ensure that the shape and width of fluorescence signals excited by different wavelengths are completely consistent. The functional blocks of the whole optical system are designed in an integrated way, and the installation of each module can be completed at one time, which is more convenient for installation or replacement; the optical module has high overall integration and simplified structure. The accuracy of installation position is ensured through accurate optical path calculation and mechanical processing.