With the proposal of the carbon peak and carbon neutrality goals, it is certain that carbon reduction and net-zero carbon emissions will be the focus of China' s medium and long-term economic and social development. As a major manufacturing country in the world, China is highly dependent on energy when it seeks to develop the industrial chain of its manufacturing industry. This article studied the transmission mechanism of how the carbon tax policy affected the industrial chain of China' s manufacturing industry under the dual carbon goals and how to give play to the government' s guiding role and do a good job in promoting carbon emission reduction and industrial chain resilience. The results of the current study are expected to be of great significance to the overall planning of China' s economic security and development, the promotion of the transformation and upgrading of the country' s manufacturing industry, and the assurance of stable and sustainable development. Based on China' s multi-regional input-output table in 2017, this study conducted a counterfactual analysis of the carbon tax policy by using the gross value accounting method and the value-added accounting method. The research found that: The industrial chain of China' s manufacturing industry in 31 provinces and cities showed significant local correlation, indicating that the correlation between industrial chains was sensitive to trade costs. Both the carbon tax policy based on the gross value accounting method and the value-added accounting method would lead to the fluctuation of the industrial chain of China' s manufacturing industry, but the carbon tax policy based on the gross value accounting method had a greater impact on the fluctuation of the industrial chain. The results of the counterfactual simulation analysis showed that the carbon tax policy based on the gross value accounting method could not avoid the accumulation of policy costs and asymmetric emission reduction along the industrial chain, which led to the phenomenon of inter-regional carbon transfer. The carbon tax policy based on the value-added accounting method could overcome the externalities of inter-regional and inter-industrial policies more effectively and avoid the carbon leakage of the industrial chain to a certain extent, which was conducive to achieving carbon equality in policymaking. Further research showed that under the framework of carbon tax policy based on the value-added accounting method, there existed an optimal carbon tax rate, which made the impact of carbon tax policy on the industrial chain of China' s manufacturing industry minimal. Based on the results of the above research, this article suggests that it is necessary for policymakers to improve the carbon emission accounting scheme and explore the schemes for the governance of the whole industrial chain system and inter-regional collaborative governance under the dual carbon goals. [ABSTRACT FROM AUTHOR]