A control system for a vehicle comprising a prime mover, a drive wheel, a manual transmission that is configured to change a gear position by a shift operation of a driver, a clutch provided between the prime mover and the manual transmission in a transmission path of transmitting a rotation force from the prime mover to the drive wheel, and a clutch actuator configured to engage and disengage the clutch, the control system comprises: a control part configured to control the clutch actuator to switch between an engaged state where the clutch is engaged and a disengaged state where the clutch is disengaged, wherein the control part is configured to provide a first shift mode in which the clutch is switched to the disengaged state before changing of the gear position and the clutch is switched to the engaged state after changing of the gear position, characterized in that the control part is configured to provide a second shift mode in which an output of the prime mover is adjusted while the clutch is kept in the engaged state during the shift operation, and either the first shift mode or the second shift mode is selected on the basis of a detection result on whether the shift operation is a shift-up operation or a shift-down operation and a traveling state according to acceleration/deceleration of the vehicle or a traveling state according to drive state/boundary state/driven state of the vehicle, wherein in the drive state a rotation force larger than a first value is transmitted from the prime mover to the manual transmission, in the boundary state a rotation force not larger than the first value is transmitted from the prime mover to the manual transmission or a rotation force not larger than a second value is transmitted from the manual transmission to the prime mover, and in the driven state a rotation force larger than the second rotation force is transmitted from the manual transmission to the prime mover. a control part configured to control the clutch actuator to switch between an engaged state where the clutch is engaged and a disengaged state where the clutch is disengaged, wherein the control part is configured to provide a first shift mode in which the clutch is switched to the disengaged state before changing of the gear position and the clutch is switched to the engaged state after changing of the gear position, characterized in that the control part is configured to provide a second shift mode in which an output of the prime mover is adjusted while the clutch is kept in the engaged state during the shift operation, and either the first shift mode or the second shift mode is selected on the basis of a detection result on whether the shift operation is a shift-up operation or a shift-down operation and a traveling state according to acceleration/deceleration of the vehicle or a traveling state according to drive state/boundary state/driven state of the vehicle, wherein in the drive state a rotation force larger than a first value is transmitted from the prime mover to the manual transmission, in the boundary state a rotation force not larger than the first value is transmitted from the prime mover to the manual transmission or a rotation force not larger than a second value is transmitted from the manual transmission to the prime mover, and in the driven state a rotation force larger than the second rotation force is transmitted from the manual transmission to the prime mover.