Cryogenic optical systems have a good capability and sensitivity in IR detection for its low thermal radiation and background noise. In the past, most of the cryogenic optical systems were reflective. It is very difficult to design refractive cryogenic optical systems because there is lack of cryogenic, infrared refractive index data. In order to make the refractive optical systems designing at cryogenic temperature possible, a cryogenic refractometer is very necessary. In this paper, a new cryogenic refractometer is described. It is obvious that this new refractometer should be integrated designed of structure, thermal and optical analysis. Based on the previous research, the integrated structure, thermal and optical analysis procedure is established. The cooling process of sample prism and acquired the temperature field of the sample prism and sample chamber are simulated. According to the results of FEA, 3 changes might happen during the cooling: the optical surface shape change of sample prism, the rigid-body movements of sample chamber, and the stress birefringence of sample prism. The changed optical surface can be fitted by a 36-terms Zernike polynomials, then the wavefront aberration of cooled sample prism can be estimated. It may cause the stress birefringence in the sample prism during its cooling, so it is very essential to estimate the change of refractive index which is due to the thermal stress. According to the final results of the analysis, the refractometer can be optimized.