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This study delves into the nexus between the efficiency of carbon emission allocation and the efficiency of green development within the context of innovative city construction. Leveraging data from 283 prefecture-level cities and corresponding provincial-level panel data spanning the period from 2005 to 2019 in mainland China, the research employs the zero-sum gain DEA model to compute provincial carbon emission allocation efficiency and allocate allowances. Furthermore, it utilizes the all-factor non-radial directional distance function and the SBM-DEA model to gauge the green development efficiency of prefecture-level cities. The double-difference method is applied to evaluate the impact of innovative city construction on regional green development efficiency. The results indicate that an imbalance between carbon emission allocation efficiency and emission quotas detrimentally affects urban green development. However, technological progress, factor accumulation, and the institutional environment associated with innovative city building mitigate this negative impact. Heterogeneity analysis reveals a differentiated effect of innovative city building on regional green development efficiency. This paper not only explores the concept of achieving an equitable distribution of carbon emission allowances but also examines how innovative city building influences regional green development. By establishing connections between urban policies, the equitable distribution of carbon emission allowances, and regional green development, it introduces a new perspective for promoting high-quality development at the regional level. [ABSTRACT FROM AUTHOR]