An engine control system is configured to improve the estimation accuracy of a fresh intake air quantity and a total intake air quantity that flows into the combustion chambers. The engine control system is configured to estimate an estimated EGR rate value Regr using a primary lag process for a target EGR rate, calculate a volumetric efficiency equivalency value based on the estimated EGR rate value Regr, estimate an estimated fresh intake air value Qac that flows into the combustion chamber based on a rate of change in a volumetric efficiency equivalency value Kin/Kin.sub.n-1 of the estimated EGR rate value Regr and the volumetric efficiency equivalency value Kin, and estimate an estimated total intake air quantity value Qsco2 that includes the EGR gas based on the estimated fresh intake air value Qac and the estimated EGR rate value Regr.