In this paper, we build up a three-dimensional model for CO2 storage in the deep reservoir. And this paper gives the mathematical formalism of combined geochemical and multi-phase flow. The results give us the information about geochemical changing caused by CO2 injection into aqueous, the dissolution or precipitation of reservoir minerals caused by aqueous components change, the change of water density, also the differences between this model and the simulation model without considering geochemical. The basic data for simulation is from York Reservoir.