In this paper, the microfluidic chips and the corresponding detection system were briefly introduced. The microfluidic chips have been widely applied nowadays, which can meet the norm of general detection instruments that must have high SNR (signal-to-noise ratio) and can detect the object at the density of 10-9 (Mol/L). The influencing factors in improvement of the SNR were mainly addressed. By studies of various detection principles, the con-focal theory and laser induced fluorescence (short for LIF) which can generate better signal and reduce stray light are finally adopted to improve SNR of the overall system; From the comparison of various optical schemes, the reflection design is chosen due to the improvement of light source efficiency and reduction of stray light; the value of the numerical aperture and the size of pinhole can be calculated by formula to exert influence on the SNR. The fluorescence wavelength scopes, was also analyzed so as to apply appropriate laser, spectral filter and PMT. Because of the need of six-way high voltage for separate control, the amplification system must be analyzed and designed to avoid influencing SNR; for better SNR, software has also been programmed.