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Promoting the green transformation of enterprises is key to achieving the goal of "double carbon" and promoting sustainable economic development. Based on 2012-2021 panel data of Chinese listed companies in Shanghai and Shenzhen, this study explores how various factors interacting with environmental management system certification (ISO14001 certification) indirectly impact enterprises' green innovation. The mechanism analysis indicates that enterprises' management system certification promotes green innovation by improving investment efficiency and alleviating financing constraints. Heterogeneity analysis demonstrates that this promotion effect of environmental management system certification on enterprise green innovation is primarily reflected in private and large-scale enterprises. Further analysis demonstrates that the implementation of the Environmental Protection Tax Law of the People's Republic of China in 2018 strengthened the system even further. Compared with state-owned enterprises, this positive effect is primarily concentrated in non-state-owned enterprises. This study provides empirical evidence to confirm the beneficial impact of environmental management system certification and environmental protection tax on corporate green innovation and provides inspiration for the promotion of this practice.