A turbocharged engine control system is provided that comprises an exhaust gas after-treatment system and a variable-capacity turbocharger. The turbocharged engine control system is configured to estimate a clogging ratio of the exhaust gas after-treatment system based on an equivalent surface area of the exhaust gas after-treatment system. A correction value is determined based on a turbine outlet pressure and the correction value is added to the clogging ratio. A target nozzle opening value is corrected such that the nozzle opening value increases as the exhaust gas after-treatment system becomes more clogged. Consequently, as the exhaust gas after-treatment system becomes clogged, the increase in pressure on the inlet side of the exhaust turbine (which acts as back pressure with respect to the engine) is suppressed and the increase in the internal EGR ratio caused by residual gas is also suppressed.