A control system and method for a hybrid construction machine is provided. The control system for a hybrid construction machine includes an engine, a hydraulic pump driven by the engine to drive a hydraulic actuator, a motor-generator driven by the engine to generate electricity and to drive the hydraulic pump as a motor supplementing the engine, an energy storage device charged with electric energy generated by the motor-generator and supplying the electric energy for motor operation of the motor-generator, a mode detector detecting a working mode of the engine, a torque detector detecting an output torque of the hydraulic pump, a memory storing upper and lower baselines of an engine torque set per working mode of the engine, and a hybrid controller comparing the detected output torque of the hydraulic pump with the upper and lower baselines set according to the detected working mode, controlling power generation of the motor-generator so that the engine is loaded as much as much as a short value if the output torque is less than the lower baseline, and controlling the motor operation of the motor-generator so that the engine output is supplemented as much as an excessive value if the output torque exceeds the upper baseline.