A comprehensive optimization study considering both system configurations and operation signals is needed for microgrid energy systems. For this, this study provides an advanced optimization based design framework that extends existing energy system optimization studies in following four aspects: complete system optimization from the beginning, comprehensive energy conversion equipment modeling, modeling of cascaded configurations, and consideration of transient loads and weather profiles. This framework aims to find optimum system configurations and operation signals for any given equipment options, and load- and weather-profiles. The framework is presented through a case study on an oceanic container transportation application. Optimized system configurations and operation signals are found under three different scenarios: minimizing life cycle cost as single objective, minimizing capital cost and annual fuel energy consumption as bi-objective, and minimizing life cycle cost considering uncertainties in load profiles. The optimized system could reduce system life cycle cost by 40% in single objective scenario and 45-52% at different levels of robustness. Exploring waste heat from the main ship propulsion engine is the key to reduce life cycle cost. The framework can be applied for a wide range of applications as an efficient tool to search for novel system designs and their evaluations. (C) 2017 Elsevier Ltd. All rights reserved.