Objective Urban-rural integration, as an important means to improve the efficiency of agricultural production factor allocation, is a key factor that influences agricultural carbon emission efficiency. Methods This study explored the effect of urban-rural integration development on agricultural carbon emission efficiency and its mechanism of action using a combination of fixed effects model, spatial autoregressive model, and threshold effect model, based on measuring the level of urban-rural integration development and agricultural carbon emission efficiency using provincial panel data from 2005 to 2020 in China. Results The study found that: (1) On the whole, urban-rural integration development had a significant negative effect on agricultural carbon emission efficiency. The mechanism test showed that urban-rural integration development helped to improve the efficiency of low-carbon technologies in agriculture, but also had a significant negative impact on frontier technological progress, which in turn was not conducive to improving the efficiency of agricultural carbon emissions. The above findings still hold true under the spatial spillover perspective. (2) From the perspective of different dimensions of urban-rural integration development, “human resource integration” can effectively improve agricultural carbon emission efficiency by improving technical efficiency. Although both “land integration” and “capital integration” had a positive impact on technical efficiency, they were negatively constrained by technological progress, which ultimately hindered the overall improvement of agricultural carbon emission efficiency. (3) The threshold econometric analysis found that the level of regional economic development was a significant threshold variable that constrained the relationship between urban-rural integration development and agricultural carbon emission efficiency. When the level of regional economic development moved past the threshold, urban-rural integration development was able to produce a significant enhancement effect on agricultural carbon emission efficiency. Conclusion Therefore, in the process of promoting integrated urban-rural development, local governments should take into account the level of regional economic development and focus on building a system and mechanism for integrating “people” as the core and “land” and “capital” as a whole. This will create the conditions for the coordinated development of urban and rural areas as an opportunity to achieve high-quality development of low-carbon agriculture.