The present invention relates to an apparatus for controlling a cascaded hybrid construction machine system and a method therefor, which apparatus includes: a control part for controlling an electric motor for driving an actuator differently according to whether or not the actuator performs a recovery action and whether or not an energy storage device can be recharged; and a motor driver for driving or stopping the electric motor by switching under the control of the control unit, wherein when the actuator performs a recovery action for both the overcharged state and the failure state of the energy storage device, the motor for driving the actuator is temporarily stopped by the switching of the motor driver so as to restrain the recovery energy generated, thus protecting the hybrid power source system and keeping the operator safe as well as resolving the problem of the working time being increased due to the system's shutting off.