The improvement of agricultural TFP is critical to promoting the high-quality development of agriculture. This paper described and identified the spatiotemporal differentiation characteristics and spatial correlation of China’s agricultural TFP in 283 prefecture-level cities from 2001 to 2018 using the Metafroniter-Malmquist and Moran index. The results showed that: (1) From 2001 to 2018, China’s agricultural TFP was 6.64%, and its growth was mainly driven by agricultural technological progress. The contribution of agricultural technological efficiency was small. The growth law showed an “inverted U-shaped” growth trend of first rising and then falling. (2) China’s agricultural TFP has significant characteristics of regional unbalanced growth. (3) The growth rate of agricultural TFP in most prefecture-level cities is medium and slow, and most prefecture-level cities relied on agricultural technological progress to promote growth. (4) The agricultural TFP of various cities showed a significant spatial correlation phenomenon of “high-high” or “low-low.” This study has significant theoretical and practical value for maintaining the stable growth of China’s agricultural TFP and promoting the high-quality development of China’s agriculture.