A system and method of controlling torque of plural variable displacement hydraulic pumps in construction equipment are provided, which can control torque of the variable displacement hydraulic pumps so that the total amount of torque of the hydraulic pumps does not exceed the preset amount of torque by presetting the torque so that the engine does not stop even at maximum load of the hydraulic pumps or by presetting the speed of the engine or the used torque of the hydraulic pumps in consideration of the fuel economy or working speed. The system includes an engine, at least two variable displacement hydraulic pumps, hydraulic actuators, control levers generating manipulation signals, control lever sensing means detecting the manipulation amounts of the control levers, hydraulic pump pressure sensing means detecting load pressures of the hydraulic pumps, maximum torque setting means setting the total torque inputted to the hydraulic pumps, desired flow rate computing means computing flow rates of the hydraulic pumps, expected torque computing means computing expected torque values of the hydraulic pumps, torque distributing means distributing torque values of the hydraulic pumps, limited flow rate computing means computing the flow rates of the hydraulic pumps, and output means outputting control signals to regulators.