The improvement of agricultural low-carbon efficiency is an important path to promote the realization of the "double carbon" goal in the Yellow River Basin. In the context of rapid urbanization development, it is of great significance to explore whether the promotion of urbanization will affect the agricultural low-carbon efficiency. Based on the panel data of 75 cities in the Yellow River Basin from 2000 to 2020, this paper uses super-DEA model, three-dimensional kernel density model and Markov chain model to measure and analyze the spatio-temporal evolution of agricultural low-carbon efficiency in the Yellow River Basin, on this basis, the panel Tobit model is used to analyze the relationship between urbanization and low-carbon efficiency in agriculture. The results show that: (1) The level of agricultural low-carbon efficiency in the Yellow River Basin is low and has not reached the effective state, showing a slow downward trend in general, among which, the agricultural low-carbon efficiency in the lower reaches is higher than that in the middle reaches, and the upper reaches is the lowest. (2) The agricultural low-carbon efficiency in the Yellow River Basin has a negative trend of transferring to the low level on the whole, and tends to maintain the original state level, and it is difficult to realize the leapfrog transfer between states. Agricultural low-carbon efficiency has obvious spatial spillover effect and "club convergence" phenomenon, high efficiency area has a positive driving effect on the neighborhood area, while low efficiency area has a negative impact on the neighborhood area. (3) The level of urbanization has a significant positive impact on the low-carbon 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. Finally, based on the above research conclusions, relevant policy recommendations were put forward, in order to provide references for promoting the improvement of low-carbon agricultural efficiency and promoting high-quality agricultural development in the Yellow River Basin.