Quantitative polymerase chain reaction (qPCR) is the most important inspection technique for virus, especially for coronavirus disease, in this year. The qPCR chip and device were planned to develop because of the characteristics of fast inspection time, high accuracy and small system volume. Therein, the fluorescence intensity was the important signal in qPCR device, which represented the positive or negative reaction after the DNA was amplified and bound on the fluorescence dye, but the fluorescence signal was easily to be affected by the excitation and scattered light. The mini spectrometer was employed to receive the fluorescence intensity in PCR chip in this study, and the optical simulation was progressed, and the stray light shutter (SLS) was added to improve the signal-to-noise ratio (SNR) of fluorescence. The analysis results showed that the SNR of fluorescence can be enhanced from 3.14 to 16.78 by using the SLS with shape of extend component aperture, which the protruding structure was at the direction away from center. The results from this manuscript can provide the important reference information to the developer of qPCR chip, whom can obtain the high SNR fluorescence signal in qPCR inspection process for disease.