A control system for an internal combustion engine provided with a plurality of cylinders, introducing air into an intake passage part extending from a throttle valve to an intake valve through the throttle valve in exactly a throttle valve air passage amount (Mt), and discharging air from the intake passage part through an intake valve in exactly a cylinder air filling amount (Mci) to fill a cylinder at the time of an intake stroke, wherein the cylinder air filling amount (Mci) is divided into a first amount of air and a second amount of air, the first amount of air being an excess of a cylinder air filling amount (Mci) with respect to a throttle valve air passage amount (Mt) occurring due to an intake stroke, wherein the control system comprises an intake pressure drop detecting means for detecting a drop in intake pressure occurring due to an intake stroke being performed, for each cylinder, a first air amount calculating means for calculating the first amount of air for a cylinder based on its intake pressure drop (ΔPmdwni); a throttle valve air passage amount detecting means for detecting a throttle valve air passage amount (Mt); a second air amount calculating means for calculating the second amount of air for a cylinder based on the throttle valve air passage amount (Mt); a cylinder air filling amount calculating means for totaling the first amount of air and the second amount of air to calculate the cylinder air filling amount for a cylinder; and a control means for controlling the engine based on the cylinder air filling amount (Mci) of the cylinder, and wherein the first air amount calculating means sets a set crank angle range so as to include the intake strokes of at least two cylinders for which cylinder air filling amounts (Mci) are to be calculated, calculates the total value of the intake pressure drops (ΔPmdwni) of the cylinders performing an intake stroke in the set crank angle range, and calculates the first amount of air based on each intake pressure drop (ΔPmdwni) and the intake pressure drop total value (∑ΔPmdwni). wherein the cylinder air filling amount (Mci) is divided into a first amount of air and a second amount of air, the first amount of air being an excess of a cylinder air filling amount (Mci) with respect to a throttle valve air passage amount (Mt) occurring due to an intake stroke, wherein the control system comprises an intake pressure drop detecting means for detecting a drop in intake pressure occurring due to an intake stroke being performed, for each cylinder, a first air amount calculating means for calculating the first amount of air for a cylinder based on its intake pressure drop (ΔPmdwni); a throttle valve air passage amount detecting means for detecting a throttle valve air passage amount (Mt); a second air amount calculating means for calculating the second amount of air for a cylinder based on the throttle valve air passage amount (Mt); a cylinder air filling amount calculating means for totaling the first amount of air and the second amount of air to calculate the cylinder air filling amount for a cylinder; and a control means for controlling the engine based on the cylinder air filling amount (Mci) of the cylinder, and wherein the first air amount calculating means sets a set crank angle range so as to include the intake strokes of at least two cylinders for which cylinder air filling amounts (Mci) are to be calculated, calculates the total value of the intake pressure drops (ΔPmdwni) of the cylinders performing an intake stroke in the set crank angle range, and calculates the first amount of air based on each intake pressure drop (ΔPmdwni) and the intake pressure drop total value (∑ΔPmdwni).