This paper uses stochastic frontier analysis to study the innovation efficiency of 83 leading listed agricultural enterprises from 2016 to 2021 in China. It is found that the innovation efficiency of China’s leading listed agricultural enterprises is not high as a whole, and although there was a slight decline during the period, it showed an overall upward trend and obvious fluctuation characteristics. Further econometric analysis is used to analyze the investment scale of innovation factors has a significant impact on the innovation efficiency of leading agricultural listed enterprises, the size and age of enterprises have a significant positive impact on innovation efficiency, and the impact of leverage level is significantly negative, and the government subsidy and equity concentration are significantly weak. The innovation efficiency of state-owned enterprises is generally higher than that of non-state-owned enterprises, and the innovation efficiency of enterprises in the eastern region is the highest, followed by the central and western regions, and the lowest in the northeast. The marginal contribution of this article may lie in: firstly, compare the innovation efficiency level of agricultural leading listed enterprises in different ownership types and registration places; secondly, construct the model of influencing factors of innovation inefficiency of agricultural leading listed enterprises to provide reference for improving innovation efficiency of agricultural leading listed enterprises.