In the sequencer based on the principle of capillary electrophoresis with laser-induced fluorescence, the polarization direction of the excitation light has an impact on the excitation efficiency of Raman scattering and fluorescence.In-depth research on this characteristic is conducted, the influence of optical systems on the polarization state of incident light through theoretical simulation modeling and polarization ray tracing is analyzed, and an experimental system to study the influence of polarization direction of excitation on the excitation results is built, in this paper. The experimental results show that the Raman scattering light intensity of POP-7 polymer as a screening medium will undergo significant changes with the change of polarization direction of excitation light, with a fluctuation value of over 50%, and this fluctuation value will correspondingly decrease with the decrease of excitation light intensity; For multi-color fluorescent dyes,they exhibit complete randomness during the excitation process. Under different concentration gradients, each color of fluorescence has its own response to changes in the polarization direction of the excitation light, but none of them show significant correlation with the polarization direction of the excitation light.