A two-conserved scalar model is proposed to model homogeneous charge compression ignition (HCCI) combustion. The model describes the reactive scalar variables in terms of the mixture fraction, Z , and the initial EGR fraction, J , where the two variables represent inhomogeneities in the fuel-air mixture and in the fresh mixture-EGR charge, respectively. The main benefits of this approach are the reduction of dimensionality in solving for the reactive scalars, and the reduced number of equations in the fluid mechanics calculation. The conserved scalar space is rediscretized at each time step by a proper zone creation strategy based on the mass distribution and reactivity in each computational cell, for which the reactive scalar variables are reinitialized in order to account for the nonlinear effect of EGR on reaction rates. The model has also been implemented into the KIVA-3v code to simulate HCCI combustion. The results show excellent agreement with experimental data, demonstrating the high fidelity and computational efficiency of the present approach.