Based on the relevant time series data of Jiangxi Province from 2000 to 2019, the dynamic relationship between agricultural science and technology innovation, technological efficiency and agricultural economic development is analyzed by using VAR model. The results show that the mutual effect of agricultural science and technology innovation on agricultural economic development is positive, while the interaction result of technological progress on agricultural economic development is complex, and the function and direction of agricultural science and technology innovation are inconsistent in different periods. Compared with technological progress, agricultural scientific and technological innovation contributes greatly to the development of agricultural economy. There is a long-term stable and balanced relationship between agricultural science and technology innovation, agricultural technology efficiency and agricultural economic growth, but the short-term impact of agricultural science and technology innovation investment on agricultural economic growth is more significant. Therefore, it is necessary to give full play to the interaction between agricultural scientific and technological innovation and technological efficiency, to promote the development of agricultural economy with scientific and technological innovation, and to promote the sustainable development of agriculture.