A control system having an isolated user computing unit, comprising: a user computing unit including a first central processing unit and peripheral circuits, and configured to execute a control program for controlling a device to be controlled using input information received from the device to be controlled to generate preliminary control information; a security computing unit including a second CPU and peripheral circuits, and configured to generate system check information using the input information received from the device to be controlled, a control program, system state information, and the preliminary control information provided from the user computing unit, compare the system check information with system state determination standard information preset by a user, directly output the preliminary control information as a final control information when it is determined that an operation state of the device to be controlled is within a normal range, and take a security action preset by the user when it is determined that the operation state of the device to be controlled is out of the normal range; and a control input/output unit connected between the device to be controlled and the security computing unit and not connected to the user computing unit and configured to receive the input information from the device to be controlled and to provide the input information to the user computing unit through the security computing unit, and further configured to provide the final control information outputted by the security computing unit to the device to be controlled, wherein the input information includes at least one of a state signal of the device to be controlled and a sensor detection signal, and the preliminary control information and the final control information include a control signal for controlling the device to be controlled a user computing unit including a first central processing unit and peripheral circuits, and configured to execute a control program for controlling a device to be controlled using input information received from the device to be controlled to generate preliminary control information; a security computing unit including a second CPU and peripheral circuits, and configured to generate system check information using the input information received from the device to be controlled, a control program, system state information, and the preliminary control information provided from the user computing unit, compare the system check information with system state determination standard information preset by a user, directly output the preliminary control information as a final control information when it is determined that an operation state of the device to be controlled is within a normal range, and take a security action preset by the user when it is determined that the operation state of the device to be controlled is out of the normal range; and a control input/output unit connected between the device to be controlled and the security computing unit and not connected to the user computing unit and configured to receive the input information from the device to be controlled and to provide the input information to the user computing unit through the security computing unit, and further configured to provide the final control information outputted by the security computing unit to the device to be controlled, wherein the input information includes at least one of a state signal of the device to be controlled and a sensor detection signal, and the preliminary control information and the final control information include a control signal for controlling the device to be controlled