A supercharging control system of an internal combustion engine comprising: a supercharger supercharging intake air using exhaust energy of the internal combustion engine; an electric motor assisting the revolution of the supercharger; a drive ratio variable mechanism changing a ratio of exhaust energy converted into the revolution of the supercharger; means for detecting that a status value (Nt) of said supercharger increases up to a target value corresponding to a target supercharging status; assist control means that controls said electric motor for the purpose of realizing the target supercharging status, while controlling said drive ratio variable mechanism with a predetermined pattern until a switching time point when the status value (Nt)of said supercharger increases up to a target value corresponding to said target supercharging status; complement control means that controls said electric motor for the purpose of generating a necessary complement torque to implement said target supercharging status or holding the revolution of said supercharger while controlling said drive ratio variable mechanism for the purpose of implementing said target supercharging status during a predetermined period after said switching time point; and non-assist control means that controls said drive ratio variable mechanism for the purpose of realizing said target supercharging status while stopping power supply to said electric motor after a time point when the exhaust energy reaches a value by which said target supercharging status can be implemented without the assist of said electric motor, wherein said complement control means includes means for reducing a command supplied to said electric motor with a predetermined pattern so that the assist force generated by the electric motor becomes zero at the end time point of said predetermined period. a supercharger supercharging intake air using exhaust energy of the internal combustion engine; an electric motor assisting the revolution of the supercharger; a drive ratio variable mechanism changing a ratio of exhaust energy converted into the revolution of the supercharger; means for detecting that a status value (Nt) of said supercharger increases up to a target value corresponding to a target supercharging status; assist control means that controls said electric motor for the purpose of realizing the target supercharging status, while controlling said drive ratio variable mechanism with a predetermined pattern until a switching time point when the status value (Nt)of said supercharger increases up to a target value corresponding to said target supercharging status; complement control means that controls said electric motor for the purpose of generating a necessary complement torque to implement said target supercharging status or holding the revolution of said supercharger while controlling said drive ratio variable mechanism for the purpose of implementing said target supercharging status during a predetermined period after said switching time point; and non-assist control means that controls said drive ratio variable mechanism for the purpose of realizing said target supercharging status while stopping power supply to said electric motor after a time point when the exhaust energy reaches a value by which said target supercharging status can be implemented without the assist of said electric motor, wherein said complement control means includes means for reducing a command supplied to said electric motor with a predetermined pattern so that the assist force generated by the electric motor becomes zero at the end time point of said predetermined period.