A fuel supply control system for a multi-fuel internal combustion engine in which a first fuel with relatively high ignitability and a second fuel with relatively low ignitability are used as fuels and the first fuel is used as an ignition source to mixedly combust the first fuel and the second fuel, the fuel supply control system for the multi-fuel internal combustion engine comprising: a first fuel supply unit which supplies the first fuel to the multi-fuel internal combustion engine; a second fuel supply unit which supplies the second fuel to the multi-fuel internal combustion engine; a first heat generation rate estimating unit (20, S102) which estimates a first heat generation rate, the first heat generation rate being a heat generation rate given when assuming that only the first fuel supplied from the first fuel supply unit is combusted in the multi-fuel internal combustion engine; an actual heat generation rate calculating unit (20, S103) which calculates an actual heat generation rate, the actual heat generation rate being a heat generation rate given when the fuels are actually combusted in the multi-fuel internal combustion engine; and a first fuel supply amount adjusting unit (20, S107, S109) which adjusts an amount of the first fuel supplied from the first fuel supply unit to the multi-fuel internal combustion engine so that a difference between the actual heat generation rate calculated by the actual heat generation rate calculating unit and the first heat generation rate estimated by the first heat generation rate estimating unit results in a predetermined target value, wherein the first fuel supply amount adjusting unit decreases the amount of the first fuel supplied from the first fuel supply unit to the multi-fuel internal combustion engine when the difference between the actual heat generation rate and the first heat generation rate is larger than the predetermined target value, and increases the amount of the first fuel supplied from the first fuel supply unit to the multi-fuel internal combustion engine when the difference between the actual heat generation rate and the first heat generation rate is smaller than the predetermined target value. a first fuel supply unit which supplies the first fuel to the multi-fuel internal combustion engine; a second fuel supply unit which supplies the second fuel to the multi-fuel internal combustion engine; a first heat generation rate estimating unit (20, S102) which estimates a first heat generation rate, the first heat generation rate being a heat generation rate given when assuming that only the first fuel supplied from the first fuel supply unit is combusted in the multi-fuel internal combustion engine; an actual heat generation rate calculating unit (20, S103) which calculates an actual heat generation rate, the actual heat generation rate being a heat generation rate given when the fuels are actually combusted in the multi-fuel internal combustion engine; and a first fuel supply amount adjusting unit (20, S107, S109) which adjusts an amount of the first fuel supplied from the first fuel supply unit to the multi-fuel internal combustion engine so that a difference between the actual heat generation rate calculated by the actual heat generation rate calculating unit and the first heat generation rate estimated by the first heat generation rate estimating unit results in a predetermined target value, wherein the first fuel supply amount adjusting unit decreases the amount of the first fuel supplied from the first fuel supply unit to the multi-fuel internal combustion engine when the difference between the actual heat generation rate and the first heat generation rate is larger than the predetermined target value, and increases the amount of the first fuel supplied from the first fuel supply unit to the multi-fuel internal combustion engine when the difference between the actual heat generation rate and the first heat generation rate is smaller than the predetermined target value.