Achieving carbon neutrality would reshape energy supply systems, and proper planning could ensure transition smoothly and reduce costs. Energy infrastructure is imperative in system planning, due to long life-span and massive investment. System planning with detailed infrastructure layout could improve the feasibility of transition blueprints, whilst the layout of carbon neutral energy supply systems and the transition pathway to carbon neutrality have not been pointed out with detailed infrastructure layout. In this study, a multi-regional, multi-period and infrastructure-based planning model is applied to describe China’s low carbon transition pathway towards carbon neutrality by 2060. The deployment of carbon neutral energy supply systems and the pathway to that are obtained by minimizing long-term system costs, and infrastructure layout and energy flows amongst regions are pointed out. Results show that power systems and hydrogen systems would dominate in the carbon neutral energy systems. To achieve carbon neutrality, existing transition targets need more efforts beyond 2030, and infrastructure investment would increase by 115 percent. Coal capacity reduction would account for most of stranded investment, and reduction of existing coal power as its life-span would be compatible with carbon neutrality.