To obtain a scientific understanding of the spatial and temporal patterns of agricultural ecoefficiency (AEE) as well as its influencing factors in Fujian Province, effective recommendations were provided to promote agricultural green development. The Super-SBM model with undesired output was employed to assess AEE, and the GTWR model was used to analyze the main factors influencing AEE based on data from nine prefecture-level cities in Fujian Province spanning from 2000 to 2020. There are three conclusions to be drawn: Firstly, the AEE of Fujian Province has increased from 0.340 in 2000 to 0.971 in 2020, but it has not yet reached the efficiency frontier due to excessive input of agricultural factors and carbon emissions. The development of AEE across regions is unbalanced with a wide gap between them. Secondly, from a spatial correlation perspective, global correlation of AEE in Fujian Province showed random distribution while local agglomeration existed to varying degrees. Thirdly, AEE in Fujian Province was influenced by various driving factors that changed significantly over different periods and exhibited obvious regional differences. In summary, the AEE of Fujian Province has shown overall improvement; however, its effectiveness remains limited. The disparities among cities are evident, necessitating the formulation of differentiated strategies for agricultural ecological development to enhance regional synergistic driving forces and improve regional AEE.