A hydraulic control system is disclosed. The hydraulic control system may have a pump, a plurality of actuators, and a plurality of valve arrangements configured to meter pressurized. The hydraulic control system may also have at least one operator input device configured to generate signals indicative of desired velocities of the plurality of actuators, and a controller. The controller may be configured to receive a pump torque limit, determine a maximum pump flow capacity, and determine desired flow rates for each of the plurality of valve arrangements based on the signals. The controller may also be configured to make a first reduction of the desired flow rates based on the maximum pump flow capacity, to make a second reduction of the desired flow rates based on the pump torque limit, and to command the plurality of valve arrangements to meter the desired flow rates after the second reduction.