This paper introduces the green technology innovation capacity under the carbon neutral goal as the dependent variable and makes research hypotheses on the digital transformation of e-commerce enterprise management and enterprise development. The research hypotheses model between the three is constructed by both quantile regression and multivariate linear regression, and the panel threshold adjustment model between green technology innovation capacity, digital transformation and enterprise development is given. Empirical evidence is used to verify the relevant influencing factors of digital specialization and enterprise development of e-commerce enterprise management under the carbon neutral goal from multiple perspectives, including correlation test, benchmark regression, quantile regression, and panel threshold adjustment test. The results show that the correlation coefficients between the potential variables of the model are all below 0.1, suggesting a significant correlation. The 1% level showed significant differences in the ability to innovate green technologies, digital transformation of e-commerce enterprise management, and high-quality enterprise development. The single threshold value of green technology innovation capacity on the ability of e-commerce enterprises to manage digital transformation is 1.6829, and the double threshold value on the high-quality development of enterprises is 0.6572 and 1.6847, respectively. The green technology innovation capacity of e-commerce enterprises needs to be strengthened under the goal of carbon neutrality in order to promote the digital transformation and high-quality development of e-commerce enterprises.