A system for controlling a continuous variable valve lift actuator of a diesel engine and a method thereof stabilize exhaust gas and improve performance by variably controlling lift and timing of intake and exhaust valves based on combustion state and driving purpose. The method may include, recognizing a driving purpose and combustion state by detecting driving conditions, temperature of exhaust gas at predetermined locations on an exhaust pipe, and NOx concentration contained in the exhaust gas, determining target position and timing of intake and exhaust valves by applying the driving purpose and the combustion state to a predetermined map table, controlling position and timing of the intake and exhaust valves by actuating a CVVA, detecting combustion pressure in a combustion chamber, and modifying fuel injection amount according to the combustion pressure.