Abstract: Promoting the digital transformation of agriculture is an essential way for cultivating the innovation momentum of specialized and new agricultural enterprises (SNAE) and realizing self-reliance in agricultural science and technology. This study examined the impact path and mechanisms of agricultural digital transformation on the innovation investment of SNAE, by employing the panel data of China’s A-share listed agricultural-related enterprises from 2015 to 2024 as research samples. The findings were as follows: First, the agricultural digital transformation significantly increased the innovation investment of SNAE, and this conclusion remained robust after applying the instrumental variable method and conducting multiple robustness checks. Second, in the mediation effect test, ESG performance played as a partial mediator between digital transformation and innovation investment, indicating that digital transformation indirectly promoted innovation investment by improving corporate ESG performance. Third, heterogeneity analysis revealed that the innovation-driven effect of digital transformation was more prominent in the samples of non-state-owned enterprises and the eastern region, with the impact coefficients being 1.3 times that of state-owned enterprises and 2.1 times that of firms in the central and western regions, respectively. This study analyzes the underlying mechanisms through which digital transformation empowers innovation investment in SNAE and puts forward relevant policy suggestions, which provide a reference for governments to formulate differentiated digital infrastructure policies for SNAE and to guide enterprises in leveraging ESG development to release digital dividends.