The precise measurement of the infrared transition of hydrogen-deuterium (HD) molecule is used to test quantum electrodynamics and determine the proton-to-electron mass ratio. The saturated absorption spectrum of the R(1) line in the first overtone (2–0) band of HD molecule has been measured by the comb locked cavity ring-down spectroscopy (CRDS) method in Hefei Tao L G, et al. 2018 Phys. Rev. Lett. 120 153001, and also by the noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS) method in Amsterdam Cozijn F M J, et al. 2018 Phys. Rev. Lett. 120 153002 . However, there is a significant difference between the line center positions obtained in these two studies. Later the discrepancy was found to be due to unexpected asymmetry in the line shape of the saturated absorption spectrum of the HD molecule. A possible reason is the superposition of multiple hyperfine splitting peaks in the saturated spectrum. However, this model strongly depends on the population transfer caused by intermolecular collisions, which is a lack of experimental and theoretical support. In this paper, the hyperfine structures of the ro-vibrational transition of HD are calculated in the coupled and uncoupled representations. The hyperfine structures of the R(0), P(1) and R(1) lines in the (2–0) band of HD molecule under different external magnetic fields are calculated. The corresponding spectral structures at a temperature of 10 K are simulated. The results show that the transition structure of HD molecule changes significantly with the externally applied magnetic field. The frequency shift of each hyperfine transition line also increases with the intensity of external magnetic field increasing. When the intensity of the external magnetic field is sufficiently high, the hyperfine lines are clearly divided into two branches, and they can be completely separated from each other. Because the dynamic effect of intermolecular collision and the energy level population transfer are very sensitive to the energy level structure, the comparison between experiment and theory will help us to analyze the mechanism of the observed special profiles. It will allow us to obtain accurate frequencies of these transitions, which can be used for testing the fundamental physics.