A control apparatus of an engine system, the engine system including an engine, a VGT configured to control a boost pressure applied to the engine by adjust an angle of a vane provided in a turbine, and an EGR valve configured to control an amount of a recirculated exhaust gas, includes a target value determiner determining a target boost pressure and a target intake air amount based on an engine speed and a fuel injection amount, an EGR valve controller calculating a target EGR mass flow rate based on the target boost pressure and the target intake air amount and determining an EGR valve opening rate, and a turbocharger controller performing a sliding mode control using the calculated target EGR mass flow rate as a parameter to calculate a target compressor power and a target turbocharger mass flow rate and determining a turbine vane opening rate.