The nature of dark matter is unknown. A number of dark matter candidates are quantum flavor-mixed particles but this property has never been accounted for in cosmology. Here we explore this possibility from the first principles via extensive N-body cosmological simulations and demonstrate that the two-component dark matter model agrees with observational data at all scales. Substantial reduction of substructure and flattening of density profiles in the centers of dark matter halos found in simulations can simultaneously resolve several outstanding puzzles of modern cosmology. The model shares the “why now?” fine-tuning caveat pertinent to all self-interacting models. Predictions for direct and indirect detection dark matter experiments are made.