Continuously tunable monochromatic light source system is a dedicated test system for radiation parameter quantitatively of CCD, it can be used to measure the relative spectral response of CCD. Compared with the conventional test apparatus, the system is possible to achieve spectral resolution of 1 nm due to the use of the high-power xenon lamp. However, the lamp introduces instability problems. The conventional time-sharing measurement method can lead to poor measurement uncertainty, and can not meet the development needs of high-precision remote sensing instrument, and then a synchronous sampling method was proposed. Combining with the comprehender of the CCD calibration theoretical model, the measurement uncertainty of two methods was analyzed. The result shows that the synchronous sampling uncertainty is better than 1.03%, which increases 43% compared with the traditional time-sharing measurement method. Otherwise, it also has a contrast testing using the two methods. As a result, the relative spectral response curve of the CCD received by the synchronous sampling method is more flat, and the standard deviation is more low, which verify the correctness of the conclusions of the analysis.