Natural gas (NG) is a promising low-carbon fuel to replace diesel for heavy-duty marine propulsion with prominent fuel cost and carbon dioxide equivalent (CDE) emissions reduction potential. However, using NG in compression ignition (CI) engines presents several inherent drawbacks. This research addresses the central issue of an NG-diesel CI engine with increased methane emissions, resulting in minor CDE emission reduction. The hydrocarbon (HC), carbon monoxide (CO), and nitrogen oxides (NOx) emissions are minimized in addition to fuel consumption and carbon dioxide emission reduction as in the current practice. The simultaneous optimizations of powertrain component sizes and the NG-engine hybrid electric propulsion control are introduced to minimize NG fuel consumption and CDE emissions globally. The top-level powertrain component sizing and bottom-level optimal power control and energy management are conducted simultaneously to achieve global optimization with balanced fuel cost and CDE emissions reductions. The new method reduced the fuel cost by about 75 percent and well-to-wake CDE emissions by about 40 percent over the traditional diesel-mechanical propulsion for the test ferry running under an actual operation profile. The research opened a new path to the global design and control optimization of the NG-diesel CI engine-powered hybrid electric marine propulsion system.