We present a new cosmological galaxy formation model, nu^2^GC, as an updated version of our previous model nuGC. We adopt the so-called "semi-analytic" approach, in which the formation history of dark matter halos is computed by N-body simulations, while the baryon physics such as gas cooling, star formation, and supernova feedback are simply modeled by phenomenological equations. Major updates of the model are as follows: (1) the merger trees of dark matter halos are constructed in state-of-the-art N-body simulations, (2) we introduce the formation and evolution process of supermassive black holes and the suppression of gas cooling due to active galactic nucleus (AGN) activity, (3) we include heating of the intergalactic gas by the cosmic UV background, and (4) we tune some free parameters related to the astrophysical processes using a Markov chain Monte Carlo method. Our N-body simulations of dark matter halos have unprecedented box size and mass resolution (the largest simulation contains 550 billion particles in a 1.12Gpch^-1^box), enabling the study of much smaller and rarer objects. The model was tuned to fit the luminosity functions of local galaxies and mass function of neutral hydrogen. Local observations, such as the Tully-Fisher relation, the size-magnitude relation of spiral galaxies, and the scaling relation between the bulge mass and black hole mass were well reproduced by the model. Moreover, the model also reproduced well the cosmic star formation history and redshift evolution of rest-frame K-band luminosity functions. The numerical catalog of the simulated galaxies and AGNs is publicly available on the web.