Farmland ecosystem service is an important output of agricultural production, but it has been incompletely reflected in current studies on eco-efficiency. In this study, the value of improved farmland ecosystem services is used as one of the expected outputs. The data envelopment method is used to evaluate the agricultural eco-efficiency (AEE) of 31 provincial administrative regions in China from 2006 to 2018. The spatial autocorrelation method is used to explore the characteristics of AEE in China. Geographical detector model (Geodetector) is adopted to detect the driving factors of AEE spatial differentiation in China. China’s AEE trend from 2006 to 2018 was downward with the efficiency value decreasing from 1.023 to 0.995. China’s AEE level has improved with an average of 1.004. The spatial distribution pattern represented in space is in the following order: eastern region > western region > northeast region > central region. The AEE gap among provinces in the western region is the largest, and that in the northeast region is the smallest. China’s AEE spatial correlation distribution presents random distribution characteristics. During the research period, the lowehigh (LH) efficiency response area has centered on Yunnan Province. The lowelow (LL) level concentration area has centered on Inner Mongolia autonomous region and Liaoning Province. The highelow (HL) level diffusion effect agglomeration area has centered on Heilongjiang Province. Energy input, water resource input, and carbon emission are the core drivers of AEE spatial differentiation in China. Water resource input, pesticide input and labor input are the significant control factors of AEE spatial differentiation in the eastern, central, and western regions of China.