In a hydraulic closed circuit system with hydraulic pumps which maintains a well-balanced flow rate by automatically controlling the flow rate, a first hydraulic pump is connected to a hydraulic cylinder device such that the hydraulic closed circuit is made, a second hydraulic pump is connected at one of paired delivery ports to a bottom side of the hydraulic cylinder device and at the other of the ports to a tank, and a prime mover drives the first and second hydraulic pumps and recovers motive power from these pumps. A pump capacity control unit detects a moving direction of the hydraulic cylinder device, and a pressure in a lower-thrust side of the device, and controls a capacity of the second hydraulic pump so that the flow rate during the extension/retraction of the hydraulic cylinder device becomes balanced between the first and second hydraulic pumps and the hydraulic cylinder device.