Under the background of coordinated development of urban agglomerations in the Yangtze River Delta, inter-city industrial transfer is frequent. Due to the connection of the economy and carbon emissions, the impact on urban carbon emission intensity has become an important strategic issue to be considered for regional low-carbon development. In this study, the dynamic shift-share model was employed to measure the amount of industrial transfer in and out of the cities. Based on the spatial global autocorrelation, the spatial Durbin model of inverse distance spatial weight matrix, and economic geographical weight matrix, this study examined the industrial transfer dynamics and the spatial-temporal evolution characteristics of carbon emission intensity of 26 cities in the Yangtze River Delta region from 2005 to 2017, and analyzed the influencing factors of urban carbon emission intensity from the spatial spillover perspective. The results show that: (1) Carbon emission intensity shows significant spatial autocorrelation and spatial spillover effects. (2) Most of the frequently transferred industries in the Yangtze River Delta urban agglomeration are non-energy-intensive industries. Industrial transfer does not produce significant carbon emission reduction effect. It is worth noting that the economic impact of industrial transfer is beginning to emerge, but industrial transfer is not conducive to carbon emission reduction. (3) The relationship between per capita GDP and carbon intensity is inverted U shaped. Technological development level and carbon intensity shows a U-shaped relationship, which indicates the"rebound effect"of the technological progress. Population growth lowers the carbon emission intensity. Proportion of the secondary industry has positive effects on carbon emission intensity. When making carbon emission reduction plans, the production efficiency, energy intensity, and human capital in different regions need to be taken into account. Local governments should monitor the carbon emission intensity when industries are transferred in and out, avoid blind transfer of industries, strengthen competitive industries, improve industrial structure, cultivate new growth points, and develop low energy consumption industry in accordance with cities'resource endowment.