Engine electrification is a critical technology in the promotion of engine fuel efficiency, among which the electrified turbocharger is regarded as a promising solution for its advantages in engine downsizing and exhaust gas energy recovery. By installing electrical devices on the turbocharger, the excess energy can be captured, stored, and re-used. The control of the energy flows in an electrified turbocharged diesel engine (ETDE) is still in its infancy. Developing a promising multi-input multi-output (MIMO) control strategy is essential in exploring the maximum benefits of electrified turbocharger. In this paper, the dynamics in an ETDE, especially the couplings among multiple loops in the air path are analyzed. Based on the analysis, a model-based MIMO decoupling control framework is designed to regulate the air path dynamics. The proposed control strategy can achieve fast and accurate tracking on selected control variables and is successfully validated on a physical model in simulations