A control system of a hybrid construction machine includes fluid pressure pumps configured to supply a working fluid to a fluid pressure actuator, a regeneration unit having a regeneration motor for regeneration to be rotated by the working fluid discharged from a load side pressure chamber of the fluid pressure actuator, a rotating electric motor coupled to the regeneration motor, and a storage battery configured to store electric power generated by the rotating electric motor, and a variable throttle configured to bleed a portion of the working fluid obtained by excluding a flow rate of the working fluid guided to the regeneration motor from the working fluid discharged from the load side pressure chamber.