In this paper, industrial structure distortion, two-way FDI and carbon emission intensity are brought into a unified research framework, and based on China's panel data from 2011 to 2020, empirical tests are conducted employing Exploratory Spatial Data Analysis (ESDA), spatial econometric model and intermediary effect test. The results show the following. Firstly, China's industrial structure distortion index shows a downward trend. The industrial structure distortion index is the highest in the west, followed by the middle, and the lowest in the East. Secondly, the relationship between carbon emission intensity and economic development shows a "decoupling" effect and keeps decreasing year by year. The spatial disparity is remarkable, showing the pattern of "the east leading, the middle catching up and the west lagging ". At the provincial level, except in Xinjiang province, the carbon emission intensity of other provinces showed different degrees of decline. In terms of spatial distribution, the polarization characteristics of carbon emission intensity are significant, and the traditional spatial distribution pattern has been broken. Thirdly, there is a positive spatial correlation between China's industrial structure distortion, two-way FDI and carbon emission intensity. The distortion of industrial structure will not only lead to the increase of local carbon emission intensity but also produce reverse spillover to adjacent areas. IFDI and OFDI provide a strong driving force for the decline of carbon emission intensity. IFDI promotes the decline of carbon emission intensity in adjacent areas, while OFDI will increase the carbon emission intensity in surrounding areas. The interaction of IFDI and OFDI can significantly reduce the carbon emission intensity of local and adjacent areas. Fourthly, the results of intermediary effect analysis show that two-way FDI is the two channels of industrial structure distortion affecting carbon emission intensity. Industrial structure distortion can affect the transmission mechanism of carbon emission intensity by affecting two-way FDI.