Worldwide efforts to switch away from coal have increased the reliance on natural gas imports for countries with inadequate domestic production. In preparing for potential gas import disruptions, there have been limited attempts to quantify the environmental and human health impacts of different options and incorporate them into decision-making. Here, we analyze the air pollution, human health, carbon emissions, and water consumption impacts under a set of planning strategies to prepare for potentially fully disrupted natural gas imports in China. We find that, with China’s current natural gas storage capacity, compensating for natural gas import disruptions using domestic fossil fuels (with the current average combustion technology) could lead up to 23,300 (95% CI: 22,100–24,500) excess premature deaths from air pollution, along with increased carbon emissions and aggravated water stress. Improving energy efficiency, more progressive electrification and decarbonization, cleaner fossil combustion, and expanding natural gas storage capacity can significantly reduce the number of excess premature deaths and may offer opportunities to reduce negative carbon and water impacts simultaneously. Our results highlight the importance for China to increase the domestic storage capacity in the short term, and more importantly, to promote a clean energy transition to avoid potentially substantial environmental consequences under intensifying geopolitical uncertainties in China. Therefore, mitigating potential negative environmental impacts related to insecure natural gas supply provides additional incentives for China to facilitate a clean and efficient energy system transition.