As critical energy hubs in power systems, substations face significant challenges in achieving net-zero operation due to the substantial carbon emissions associated with their infrastructure and operational processes. This study establishes a comprehensive carbon emission index system to evaluate and optimize the operational phase carbon footprint of substation facilities. Four functional categories were established based on the carbon emission composition of substations, and 12 key variables were identified. The analytic hierarchy process was used to determine variable weighting coefficients, while process based on life-cycle assessment combined with grey relational analysis enabled quantitative calculation of carbon indices across four representative substations. Implement carbon reduction measures for the two key variables of main transformers and air conditioning, and assess the carbon reduction effectiveness of substations based on sensitivity analysis. The results indicate that the proposed carbon index effectively characterizes operational emissions, achieving 89.7% evaluation accuracy. Deployment of high-efficiency transformers and advanced HVAC technologies demonstrated carbon intensity reductions of 28.2% and 4.4%, respectively. The developed indicator system provides dual functionality: facilitating emission diagnostics for existing facilities and guiding low-carbon design strategies for new substations. This methodology advances the development of quantitative assessment frameworks for achieving carbon-neutral substation operations in alignment with zero-energy building standards.