Abstract: The space-borne visual and infrared multispectral sensor (VIMS) can simultaneously detect multiple spectral bands in the visible, near-infrared, short-wave infrared, medium-wave infrared, and long-wave infrared spectral ranges, which plays an important role in thermal pollution emission detection and crop growth analysis. However, when light passes through the atmosphere, it is affected by atmospheric refraction, which causes different degrees of deflection in different spectral bands. It influences the geometric positioning accuracy of the image and the registration accuracy between the spectral bands, which affects the application of VIMS image. In this paper, with VIMS of GaoFen5 (GF5) the optical satellite atmospheric refractive correction model based on the measured atmospheric parameters is used to analyze the influence of atmospheric refraction on the geometric accuracy of different bands in different regions and at different times. The experimental results show that when the view angle is 45 °, the absolute geometric positioning error of the blue band caused by atmospheric refraction is about 6.491m, and the relative geometric positioning error is about 2.698m. The registration accuracy between the blue band and the long-wave infrared band spectrum can reach 0.161m. This research can provide important support for the data processing of VIMS with higher space resolution.