A control system for a hybrid construction machine, includes: a fluid pressure pump; a regeneration motor rotationally driven by refluxed working fluid; a rotating electric machine rotationally driven by the regeneration motor; an energy storage part into which regenerated electric power is charged; and a temperature detecting part adapted to detect a temperature of the energy storage part, a control part charging with regenerated electric power when a temperature of the storage part becomes below a first set temperature, until achieving a voltage higher than a charge termination voltage of when the temperature of the storage part is equal to or more than the first set temperature by an amount of internal resistance according to the temperature of the storage part.