Methane, a more potent greenhouse gas than carbon dioxide, aggravates the greenhouse effect of ecological environment through its emissions. When transporting hydrogen-mixed natural gas through urban polyethylene pipes, methane will be emitted due to the permeation characteristic of polyethylene pipe material. Therefore, it is crucial to pay attention to the methane emissions from permeation of polyethylene pipes for protecting the environment and climate. In this paper, the solubility and diffusion coefficients of methane within hydrogen-mixed natural gas in polyethylene pipe materials are calculated through the Monte Carlo method and molecular dynamics simulation to determine the permeation coefficient of methane. Simultaneously, the methane emissions and equivalent carbon dioxide emissions of the hydrogen-mixed natural gas in polyethylene pipes are investigated. Results indicate the methane solubility coefficient decreases with increasing temperature and hydrogen mixing ratio. The methane diffusion and permeation coefficients increase with the rising temperature and pressure, and decreasing hydrogen mixing ratio. The pressure exerts minor influence while the temperature and hydrogen mixing ratio have more significant impact. That is, the lower the temperature and the higher the hydrogen mixing ratio, the less methane emissions caused by permeation. Therefore, the effective reduction of methane emissions can be achieved by adding the insulation layer to mitigate the impact of high temperature and increasing the hydrogen mixing ratio. For example, for the polyethylene pipe with the operating pressure of 4 bar and the size specification of SDR11, when the temperature drops from 300 K to 260 K, the methane emissions of hydrogen-mixed natural gas with hydrogen mixing ratios of 0 vol%, 20 vol%, 50 vol% and 80 vol% will be drastically reduced by 73.3%, 74.4%, 77.2% and 78.5% respectively, and when 20 vol%∼80 vol% hydrogen are mixed in the natural gas at 260 K, 300 K and 310 K, the methane emissions will be effectively reduced by 26.7%∼85.6%, 23.3%∼82.1% and 23.9%∼82.4% respectively. The findings of this study can serve as guidance for reducing the methane emissions from permeation of polyethylene pipes transporting hydrogen-mixed natural gas.