Green innovation integrates innovation-driven and green development strategies, which helps to realize the green transformation of production and life in the Yangtze River Delta region, and promote high-quality economic development. Based on the multidisciplinary cross attribute of system dynamics (SD), the boundary and influencing factors of the green innovation system are defined, and the system dynamics model of green innovation ability of science and technology enterprises is constructed. With the help of statistical data from 2010 to 2020, the model is simulated to explore the change trend and law of elements. The results show that: (1) The green innovation ability of science and technology enterprises is composed of three stages, knowledge innovation, technological innovation, and innovation application, which are interconnected and progressive. The change trend of each variable is conducive to the improvement of green innovation competitiveness, and the green innovation benefits are significant. (2) Green innovation is driven by multidimensional factors such as R&D investment, technological innovation investment, knowledge innovation ability, and the conversion rate of scientific research achievements. The improvement of the conversion rate of scientific research achievements has the greatest impact on the enterprise’s green innovation ability, and the change trend is more obvious. (3) Positive and negative two-direction sub-mode regulation of R&D investment, technological innovation investment, and scientific research achievement conversion coefficient will affect the speed of green innovation accumulation of enterprises, and this increment is marginally increasing with the increase of the coefficient in the short term. Finally, some suggestions are put forward to promote the green innovation ability of science and technology enterprises in the Yangtze River Delta.