A differential drive system having individual clutch control and mutual flexibility transmission, which utilizes a rotary kinetic power source to directly drive a first transmission device, comprising: output end transmission devices (T100, T200) individually installed between the output end of the first transmission device and two or more loading wheel sets driven thereby, individually installed for driving the loading wheel sets arranged at two sides of a common load body, so as to drive the combined common load body; individually-controlled output end clutch devices (CL100, CL200) are installed for driving the output end transmission devices (T100, T200), the driven wheel sets (W100, W200), and wheel shafts (S101, S102) to perform engaging transmission or terminating transmission; a flexibility transmission device disposed between the wheel shafts (S101, S102) of the loading wheel sets (W100, W200) axially defined at two lateral sides of the common load body; the flexibility transmission device composed of a dual shaft connecting device having slip coupling torque, so that when controlling one of the individually-controlled output end clutch devices (CL100, CL200) to perform engaging transmission and controlling the other output end clutch device (CL100, CL200) coaxially at the opposite side to perform terminating transmission with differential rotational speed from the engaging transmission side to the terminating transmission side, the rotational speed of the wheel set (W100, W200) at the terminating transmission side of the output end clutch device is lower than that of the wheel set (W100, W200) at the engaging transmission side, but still equipped with the driving power in a lower speed; further comprising an external operation interface; a control unit; characterized by comprising a direction changing signal sensor, wherein, when changing directions, the signal of the direction changing signal sensor can be sent, together with the signal of the external operation interface, to the control unit for controlling the relative speed ratio switching of the output end transmission device and the output end transmission device. output end transmission devices (T100, T200) individually installed between the output end of the first transmission device and two or more loading wheel sets driven thereby, individually installed for driving the loading wheel sets arranged at two sides of a common load body, so as to drive the combined common load body; individually-controlled output end clutch devices (CL100, CL200) are installed for driving the output end transmission devices (T100, T200), the driven wheel sets (W100, W200), and wheel shafts (S101, S102) to perform engaging transmission or terminating transmission; a flexibility transmission device disposed between the wheel shafts (S101, S102) of the loading wheel sets (W100, W200) axially defined at two lateral sides of the common load body; the flexibility transmission device composed of a dual shaft connecting device having slip coupling torque, so that when controlling one of the individually-controlled output end clutch devices (CL100, CL200) to perform engaging transmission and controlling the other output end clutch device (CL100, CL200) coaxially at the opposite side to perform terminating transmission with differential rotational speed from the engaging transmission side to the terminating transmission side, the rotational speed of the wheel set (W100, W200) at the terminating transmission side of the output end clutch device is lower than that of the wheel set (W100, W200) at the engaging transmission side, but still equipped with the driving power in a lower speed; further comprising an external operation interface; a control unit; characterized by comprising a direction changing signal sensor, wherein, when changing directions, the signal of the direction changing signal sensor can be sent, together with the signal of the external operation interface, to the control unit for controlling the relative speed ratio switching of the output end transmission device and the output end transmission device.