The effect of digital transformation on enterprise technological innovation is reflected in quantity and quality, which may show heterogeneity. In this regard, this paper uses the data of China’s A-share agricultural listed companies from 2015 to 2020 to compare the differential impact of enterprise digital transformation from the perspective of quantity and quality of technological innovation. Firstly, the Tobit model is used to test whether there are differences in the impact of digital transformation on the quantity and quality of technological innovation of agricultural enterprises, and heterogeneity is tested according to the nature of enterprises. Secondly, this paper explores the reasons digital transformation has different effects on the quantity and quality of technological innovation through mechanism analysis. Finally, according to the threshold model, the conditions for digital transformation to promote the quantity and quality of technological innovation of agricultural enterprises are discussed. The empirical results show that, first, the digital transformation of agricultural enterprises only promotes the number of technological innovations, and there is heterogeneity in the nature of enterprises, but the innovation efficiency is not affected. Second, the period expense rate will lead to digital transformation, having different effects on the quantity and efficiency of technological innovation of agricultural enterprises. Third, the impact of digital transformation on the technological innovation efficiency of agricultural enterprises has a significant single threshold effect, and when the period expense rate is less than the threshold, the digital transformation has a significant role in promotion.