The molecular hydrogen (H<sub>2</sub>) in the troposphere is highly influenced by the strength of H<sub>2</sub> uptake by the terrestrial soil surface. The global distribution of H<sub>2</sub> and its uptake by the soil are simulated by using a model called CHemical AGCM for Study of Environment and Radiative forcing (CHASER), which incorporates a 2-layered soil diffusion/uptake process component. The simulated distribution of deposition velocity over land reflects regional climate and has a global average of 3.3 × 10<sup>−2</sup> cm s<sup>−1</sup>. In the region north of 30° N, the amount of soil uptake increases, particularly in the summer. However, the increase in the uptake becomes smaller in the winter season due to snow cover and a reduction in the biological activity at low temperatures. In the temperate and humid regions in the mid- and low-latitudes, the uptake is mostly influenced by the soil air ratio, which controls the gas diffusivity in the soil. In the semi-arid region, water stress and high temperature contribute to the reduction of biological activity, as well as to the seasonal variation in the deposition velocity. The comparison with the observations shows that the model reproduces both the distribution and seasonal variation of H<sub>2</sub> relatively well. The global burden and tropospheric lifetime are 150 Tg and 2.0 yr, respectively. The seasonal variation of H<sub>2</sub> in the northern high latitude is mainly controlled by the large seasonal change in soil uptake. In the Southern Hemisphere, the seasonal change in the net chemical production and inter-hemispheric transport are the dominant cause of the seasonal cycle. Large biomass burning impacts the magnitude of seasonal variation mainly in the tropics and subtropics. Both observation and model show large inter-annual variation, especially for the period 1997–1998, associated with the large biomass burning in tropics and northern high-latitudes. The soil uptake shows relatively small inter-annual variability compared to the signal from biomass burning. We note that the thickness of biologically inactive layer near the soil surface and the uptake flux in semi-arid region is important for the current and future budget of atmospheric H<sub>2</sub>.