Ratifying the Paris Climate Change Agreement of 2015, which is the new framework for global environmental measures for change after 2020 onward, Japan is proposing to reduce its greenhouse gas emissions by 26% by 2030 from 2013 levels. To achieve this target, it is indispensable to transcend the current fossil-fuel-based technologies (petroleum, coal, and natural gas) and shift to renewable energy systems. Neutral fuels or fuels free of carbon dioxide emissions must become the predominant source of energy, in addition to introducing energy conservation technologies in manufacturing, transportation, business, and households. Amid these developments, fuel cell vehicles and hydrogen production technologies are gaining much attention. Our research group is developing a new hydrogen-generating system that directly decomposes hydrogen from methane and separates carbon as a solid substance with zero carbon dioxide emissions. We estimate the carbon dioxide reduction effect of our new hydrogen-generating system and compare it with the current steam reforming method by applying scenario input–output analysis. Our new system is expected to lower carbon dioxide emissions to 14.1% of the conventional system in the industrial sector. With the replacement effect of gasoline vehicles to fuel cell vehicles, carbon dioxide emissions are expected to reduce for both hydrogen production technologies. The new system is more efficient and saves carbon dioxide emissions by 21.7% more than the conventional system, under the assumption that 800 thousand fuel cell vehicles will be available in Japan before 2030.