The manufacturing industry is the backbone of the national economy, but it is also a significant source of environmental pollution emissions. In order to reduce pollutant emissions and protect the environment, China has implemented an environmental protection tax policy. In this context, this paper investigates the impact of environmental protection tax on the economic, environmental, and social sustainability of the manufacturing supply chain. The findings are as follows. Firstly, the environmental protection tax will reduce supply chain profits and decrease the economic sustainability of the manufacturing industry supply chain. Secondly, the environmental protection tax will reduce the environmental damage caused by pollutant emissions, and enhance the environmental sustainability of the manufacturing industry supply chain. However, excessive environmental protection tax may have negative effects. Thirdly, the environmental protection tax will increase prices, decrease consumption, and reduce consumer surplus, which is not conducive to the social sustainability of the manufacturing industry supply chain. Although environmental protection tax reduces supply chain profits and consumer surplus, it will improve the living environment, promote green consumption, and contribute to sustainable development.