Scientifically characterizing the intrinsic mechanism of the biased reduction targets affecting agricultural green innovation is of great practical significance for the systematic promotion of the greening transformation of China's agricultural development mode. This paper first constructed a two-sector endogenous economic growth model, theoretically deducing the intrinsic mechanism by which the bias reduction targets were adjusted through the green transformation of agricultural production input factors, which in turn affected the research and development decision-making of the agricultural innovation sector. To the end, this paper treated the strategy of zero growth in synthetic fertilizer use (ZGS) implemented in 2015 as a policy shock and empirically assessed its green innovation effect using the staggered difference-in-differences model. The results showed that ZGS significantly contributed to the increase of green patents in Chinese agriculture. The above conclusion still held after a series of robustness tests, including using terrain complexity as an instrumental variable, estimating the robust staggered difference-in-differences model, eliminating policy interference, altering the estimated model, and replacing the explanatory variables. However, the obvious regional heterogeneity of this effect was reported: the higher the level of marketization and digitalization, the fuller the release of this innovation effect; and that ZGS was more significant in inducing the green innovation activities of enterprises and individuals than of innovation bodies such as universities and research institutions. Finally, this paper also empirically tested the two paths of the theoretical model about the green innovation effect triggered by the biased reduction targets. The study confirmed that the green innovation effect of ZGS mainly resulted from two channels: the expansion of the market scale for agricultural green technologies and the green-oriented allocation of innovation resources. The above conclusions imply that it is necessary to create a sound innovation ecology by strengthening the innovation of green science and technology institutions and combining active government with an effective market. Particularly, a portfolio of policy instruments, including the fiscal, taxation, financial, investment, price policy, and standard system concerning green technology development, should be created to guarantee green technology development. In addition, ZGS can set up differentiated reduction targets considering regional endowment conditions to ensure its smooth progress. [ABSTRACT FROM AUTHOR]