We construct the radially-resolved semi-analytic models of galaxy formation based on the L-Galaxies model framework, which include both atomic and molecular gas phase in ISM. The models run on the halo outputs of ΛCDM cosmology N-body simulation. Our models can reproduce varies observations of HI gas in nearby galaxies, e.g. the HI mass function, the HI-to-star ratio vs stellar mass and stellar surface density, universal HI radial surface density profile in outer disks etc. We also give the physical origin of HI size-mass relation. Based on our model results for local dwarf galaxies, we show that the “missing satellite problem” also exists in the HI component, i.e., the models over-predict dwarf galaxies with low HI mass around the Milky Way. That is a shortcoming of current ΛCDM cosmology framework. Future survey for HI gas in local dwarf galaxies (e.g. MeerKAT, SKA & FAST) can help to verify the nature of dark matter (cold or warm).