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Improving carbon emission efficiency and narrowing the gap of efficiency between cities are vital for achieving collaborative emission reduction. Based on the perspective of spatial imbalance, this study constructs an empirical analysis framework of "gap explains gap", quantitatively analyzes the impact of spatial imbalance of green technological innovation and industrial structure upgradation on the carbon emission efficiency gap through quadratic assignment procedure analysis method. The results are as follows: (1) The urban carbon emission efficiency is generally low and shows a decreasing trend. The carbon emission efficiency shows a "step-like" distribution pattern from coastal to inland regions. Some economically developed cities such as Beijing, Shanghai, Guangzhou, Shenzhen, Hangzhou, and Nanjing have high CEE. (2) The difference in urban carbon emission efficiency first decreases and then increases, and the inter-regional gap is the key to narrowing the overall gap in the future. (3) The full-sample regression shows that an increase in the spatial imbalance of green technological innovation, industrial structure rationalization, and industrial structure advancement will increase the carbon emission efficiency gap, but the impact is smaller than that of the energy intensity gap. (4) In terms of period, the influence of industrial structure advancement gap economic development level gap, and energy intensity gap is decreasing, while the influence of green technological innovation gap and industrial structure rationalization gap is increasing. As the impact of green technological innovation gap increases the largest, it will become the primary factor affecting the carbon emission efficiency gap in the new era. (5) In terms of region, the dominant factor affecting the carbon emission efficiency gap in the eastern and central regions is the energy intensity gap, whereas that in the western regions is the economic development level gap. This study theoretically enriched the study of carbon emission efficiency and made up for the shortcomings of previous studies that only focused on efficiency and ignored the efficiency gap. And this study has important reference significance for policymakers in accurately formulating strategies to narrow the gap in carbon emission efficiency and cooperatively improve urban carbon emission efficiency. [ABSTRACT FROM AUTHOR]