This study focuses on the national-level green factory certification program. Drawing on panel data of Chinese A-share listed manufacturing firms from 2004 to 2024 and employing a difference-in-differences (DID) approach, it investigates the impact of green factory certification on corporate green innovation and examines the underlying mechanisms, with the aim of providing empirical support and policy insights for the green transformation of the manufacturing sector. The findings are as follows. First, inclusion in the green factory list promotes both radical and incremental green innovation. However, firms show a stronger inclination toward deepening exploration within their existing knowledge base, as evidenced by an increase in patent output. Meanwhile, knowledge recombination exhibits a certain degree of concentration. Second, green factory certification significantly stimulates green innovation in traditional industries and non-heavily polluting sectors, but has no significant effect on firms in high-technology industries or heavily polluting sectors. Third, green factory certification facilitates corporate green innovation through two channels: internal drivers and external support. On the one hand, it strengthens environmental investment and fosters green awareness; on the other hand, it expands financing channels and attracts green capital.