With the urgent goal of increasing student retention within science, technology, engineering, and mathematics (STEM) fields, STEM identity is highlighted as a powerful source of student persistence. Since chemistry is an important part of the STEM discipline, a growing body of research has focused on chemistry identity. However, we currently know very little about how to improve students' chemistry identity. Therefore, the present study aimed to explore the mechanisms of metacognition, learning burnout, and learning flow in identity in the context of chemistry, further providing suggestions for the advancement of students' chemistry identity. Based on previous studies, the current study hypothesized that chemistry learning burnout and flow would play a chain mediating role in the relationship between metacognition and chemistry identity. A sample of 594 tenth-grade students completed questionnaires for the assessment of the four main variables in this study. The results showed that (1) metacognition, chemistry learning burnout, and chemistry learning flow significantly predicted students' chemistry identity after the effect of gender was controlled; (2) both chemistry learning burnout and chemistry learning flow played separate mediating roles in the relationship between metacognition and chemistry identity; and (3) the chain mediating effect of metacognition [right arrow] chemistry learning burnout [right arrow] chemistry learning flow [right arrow] chemistry identity was significant. These findings imply that embedded metacognitive prompts, decreased learning burnout, and increased flow experience are vastly helpful in developing learners' chemistry identity. Finally, we further highlight the educational implications of the findings of this study and propose lines of future research.