An object of the present invention is to provide a control system for a multi-fuel internal combustion engine capable of using gaseous fuel and liquid fuel, with which variation in an air-fuel ratio of an air-fuel mixture following a switch in the fuel used by the internal combustion engine is suppressed. To achieve this object, the present invention provides a control system for a multi-fuel internal combustion engine capable of using gaseous fuel and liquid fuel, in which, when the fuel used by the internal combustion engine is switched, an amount of burned gas remaining in a cylinder before and after the switch is modified, whereby variation in an amount of wall surface adhered fuel is suppressed using heat of the residual gas.