Based on the carbon emission data of China’s manufacturing industry from 1998 to 2015, this paper examines the impact of carbon emission inclination of the central and local governments’ industrial planning on regional carbon emissions. The findings of this study suggest that central industrial planning focuses on the long-term goal of economic development and favors low carbon emission industries, while local governments are more inclined to short-term economic growth and focus more on high-carbon emission industries with high output. The support of local industrial planning for high-carbon emission industries can reduce the intensity of regional carbon emissions, while the influence of central industrial planning is not evident. The mechanism analysis shows that government support for some industries can improve the industrial added value and reduce the carbon emission intensity. As the output value and carbon emission level of high-carbon emission industries are higher, the decline of carbon emissions caused by local government support for high-carbon emission industries will eventually lead to the reduction of carbon emission intensity in the whole region. The research explains the different paths that the central and local governments choose to develop a low-carbon economy and analyses their influences.