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Purpose: Improving agricultural carbon-output efficiency is an important path to realize the “double carbon” goal in the Yellow River Basin. In the context of rapid urbanization development, it is significant to explore whether promoting urbanization will affect agricultural carbon-output efficiency. Methods: Based on panel data of 75 cities in the Yellow River Basin from 2000 to 2020, this paper uses the super-DEA model, three-dimensional kernel density model, and Markov chain model to measure and analyze the spatio-temporal evolution of agricultural carbon-output efficiency in the Yellow River Basin. The panel Tobit model is used on this basis to analyze the relationship between urbanization and carbon-output efficiency in agriculture. Results: The results show the following: (1) The level of agricultural carbon-output efficiency in the Yellow River Basin is low and has not reached an effective state, showing a slow downward trend in general where the agricultural carbon-output efficiency in the lower reaches is higher than that in the middle reaches, and the upper reaches has the lowest. (2) Agricultural carbon-output efficiency in the Yellow River Basin has a negative trend of transitioning to a low level overall and maintaining its original level, and it is difficult to realize the leapfrog transfer between states. Agricultural carbon-output efficiency has an obvious spatial spillover effect and “club convergence” phenomenon; the high-efficiency area has a positive driving effect on the neighborhood area, while the low-efficiency area has a negative impact on the neighborhood area. (3) The level of urbanization has a significant positive impact on the carbon-output efficiency of agriculture in the upper, middle, and lower reaches of the Yellow River Basin, which plays an important role in promoting the green development of agriculture.