China has limited arable land area, and its output value is increased with enhanced agricultural inputs such as machinery, irrigation, fertilizers, and pesticides. However, this mode is accompanied by an increase in agricultural carbon emissions. With the aim to further examine the driving effect of scientific and technological innovation on economic growth and green agriculture, this study uses the Solow growth model coupled with the Cobb–Douglas production function and vector autoregressive models. Then, the agricultural scientific and technological innovation capacity in Guangdong Province during 2006–2020 is evaluated by using the contribution rate of agricultural scientific and technological progress (ASTP) as the assessment index. In addition, the carbon footprints of green agricultural indexes such as machinery, irrigation, fertilizers, and pesticides are measured to analyze the relationship between green agriculture and agricultural scientific and technological innovation capacity. Results demonstrate the gradual increase in the contribution rate of ASTP in Guangdong Province. During the 11th, 12th, and 13th Five-Year Plan periods, the rates were 65.09%, 65.94%, and 70.40%, respectively, indicating that the agricultural scientific and technological innovation ability constantly improved. Among the indexes of green agriculture, the carbon footprints of machinery have a significant impact on agricultural scientific and technological innovation, which is quickly transformed into machinery. Such innovation requires the driving force of science and technology itself, which have relatively significant and rapid effects. On the basis of the results, corresponding policy suggestions are proposed: increasing investments in scientific and technological innovation in the agricultural field, vigorously developing new energy-saving and emission reduction products and processes for fertilizers, and increasing the research and promotion of agricultural machinery. The proposed method provides good prospects for the development of agricultural production towards mechanization, intelligence, efficiency, and greenness.