By building an agricultural economic development evaluation index system, this paper analyzed the agricultural economic development level of China and its eastern, central and western regions, from 2000 to 2016. In addition, by applying the Thiel index, the exploratory spatial data analysis and panel regression model, this paper also explored the provincial regional differences, the spatial-temporal evolution patterns and the driving mechanism of agricultural economic development in China. Results showed that: 1) from 2000 to 2016, the levels of agricultural economic development in China and in the eastern region, the central region, and the western region could be roughly divided into the period of sustained growth from 2000 to 2011 and the basic stabilization phase from 2012 to 2016, and showing an obvious descending trend from the east to the west; 2) during the study period, the inter-regional gap was the main reason in driving the development of China’s agricultural economy. However, after 2007, the intraregional gap had gradually expanded, and in 2015, it had become the main reason for the regional differences; 3) China’s agricultural economic development had obvious spatial agglomeration characteristics, and its spatial pattern was more complicated from 2000 to 2008, while from 2008 to 2016, it basically showed a relatively stable diminishing trend from the east to the west; and 4) economic growth was the primary driving factor for regional agricultural economic development and it played a greater role than industrialization and precipitation. While urbanization and multiple cropping index had certain negative impacts on regional agricultural economy. Additionally, agricultural economic development had obvious spatial dependences and spillover effects, which could produce polarization across regions.