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Air intake and fuel supply conditions are the major factors that affect diesel engine performance at plateau. In a regulated two-stage turbocharged diesel engine, these parameters are reflected as the adjustment of fuel injection mass (mfuel), fuel injection advance angle, and bypass valve opening of a high-pressure stage (HP) turbine. Due to the strongly nonlinear nature and complexity of the diesel engine, it is difficult to find the proper parameter combinations. That is why a model-based optimization method is adopted in this paper. The simulation model of a six-cylinder two-stage turbocharged diesel engine is built on the GT-SUITE platform. According to the analysis of diesel engine operation characteristics at high altitude, a fuzzy optimization algorithm is proposed based on a fuzzy logic controller and is realized in a MATLAB/simulink (MATLAB 2014, Mathworks, Natick, MA, USA) environment. Joint optimization of air intake and fuel supply parameters is then performed on the GT-MATLAB co-simulation platform. Results show that engine torque at full load is significantly increased. At the full load point of 2100 r/min, engine power is increased from 256.5 to 319.6 kW, and brake specific fuel consumption (BSFC) is reduced from 243.1 to 222.3 g/(kW·h). Peak torque is increased from 1944.8 to 2173.2 N·m. [ABSTRACT FROM AUTHOR]