Modular Multilevel Converters (MMC) are being widely considered for medium to high voltage DC generation systems. Integrated system design optimization of the generator-MMC system through multi-objective optimization is of interest, because such an approach allows the trade-off between competing objectives (for example, mass and loss) to be explicitly and quantitatively identified. In this work, such an optimization based design paradigm for MMC based generator rectifier systems is developed. To formulate the design problem as a multi-objective optimization problem, it is required that the system waveforms can be obtained to facilitate the imposition of constraints and the estimation of power losses. Similarly, it is also desired to include detailed electric machine magnetic and electrical analysis in design optimization, as well as aspects such as the inductor and heat sink design. Such development typically requires detailed component design and simulation models for the electric machine and converter which are computationally expensive. As an alternative, the proposed work utilizes an electric machine metamodel, heat sink metamodel, and high-speed steady-state simulation model for the MMC to facilitate multi-objective optimization minimizing system metrics of interest while satisfying system constraints. Using the developed component simulation and design models, a multi-objective optimization based design of an MMC based generator-rectifier system is conducted.