I study structure formation in the Universe and galaxy formation in cosmological context. I use cosmological hydrodynamic simulations to study how the large-scale structure in the Universe, galaxies and supermassive black holes have evolved in this Universe which is dominated by dark energy and dark matter. By comparing the results of numerical simulation and the observations by large telescopes such as Subaru and Hubble Space Telescope, we are able to put constraints on the theories of structure formation and cosmological models. Some of the current research project includes: 1) the distribution of baryons and metals in the Universe and giving theoretical inputs toward PFS survey by Subaru telescope; 2) radiation hydrodynamic simulations of supermassive black hole seed formation in the early Universe.