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This paper describes a hybrid robust nonlinear control approach for modern diesel engines operating multiple combustion modes; in particular, low temperature combustion and conventional diesel combustion modes. An innovative control system is designed to track different key engine air-path operating variables at different combustion modes as well as to avoid singularity which is inherent for turbocharged diesel engine running multiple combustion modes. The overall system consists of a finite-state machine-based supervisory controller and multivariable sliding mode controllers with integral actions in sliding surfaces for different combustion modes. The system controlled outputs for different combustion mode controllers are carefully chosen with respect to combustion characteristics as well as sensor/measurement limitations. The performance of the control system is evaluated on a modern light-duty diesel engine. Experimental results demonstrate significant merits of the proposed control system compared against those obtained by conventional mapping/calibration-based approaches.