The coupled system of multilayer dynamics of fluids in porous media is to describe the history of oil-gas transport and accumulation in basin evolution. It is of great value in rational evaluation of prospecting and exploiting oil-gas resources. The mathematical model can be described as a coupled system of nonlinear partial differential equations with moving boundary values. A kind of characteristic finite difference schemes is put forward, from which optimal order estimates in norm are derived for the error in the approximate solutions. The research is important both theoretically and practically for the model analysis in the field, the model numerical method and software development.