Growing concern over the energy crisis and climate change has driven the advancement of distributed energy systems focused on high efficiency, low cost, and environmental sustainability. Methanol reforming proton exchange membrane fuel cells (PEMFCs), with their stable operation, low fuel storage and transportation costs and high efficiency, emerge as promising candidates for distributed energy systems. However, carbon emissions from the methanol conversion process pose significant challenges. This study develops a novel methanol reforming PEMFC-based distributed cogeneration system integrated with carbon capture and utilization, based on the methanol conversion and regeneration (Methanol -> Hydrogen + Carbon dioxide -> Methanol), achieving nearly zero emissions while generating cooling, heating, and electricity. The proposed system achieves the energy efficiency of 87.25 %, exergy efficiency of 34.20 %, a levelized cost of electricity of 0.255 $/kWh and direct carbon emissions approaching zero. Compared to conventional cogeneration system, it reduces emissions by nearly 100 %, lowers the levelized cost of electricity of 21.78 %, and increases energy and exergy efficiencies by 3.54 % and 0.94 %, respectively. Compared with the previous systems with carbon capture and storage, it shows a 3.96 % higher energy efficiency and a 1.64 % higher exergy efficiency. This novel system provides an integrated approach for methanol fuel-based cogeneration systems, enhancing sustainability and efficiency.