Bio-natural gas (BNG) has received recent interest as a renewable alternative to natural gas (NG). BNG supply chains (BSC), including production, transportation, and utilization, are compatible and can overlap with existing NG infrastructure. The goal is to develop a set of models that achieve the various trade-offs between economic, environmental and safety risks by combining life cycle assessment (LCA), mixed-integer linear programming (MILP) and fuzzy optimization, expanding the utilization of BSC while quantifying the risk of the whole process, so as to improve the safety awareness of the project operation. BNG technologies were considered: anaerobic digestion (AD), gasification, and syngas methanation. This model can analyze the changes in the different objectives of each module and the distribution of biomass mass flow by comparing different straw-based harvesting rates. Results indicate that AD technology possesses the lowest economic cost, and BNG as transportation fuel will generate the most benefits. The unit cost of BNG for different technologies ranges from 0.36 to 0.67 $/m³,the emission reduction is from 5.18 kg/m³ to 10.28 kg/m³,and the maximum safety risk value is 1.96. The proposed model was applied to a case study in China to illustrate the optimization of a regional straw-based BSC. The results illustrate how BNG supply chains can be systematically planned as part of an integrated decarbonization policy while mitigating safety risks that may occur from handling this fuel.