Creativity is a universal core higher-order cognitive ability in the 21st century, which reflects a country’s core competitiveness and soft power. Mindfulness, as an important concept in positive psychology, has also received attention for its potential effect on research creativity. Using structural equation modeling and bootstrap methods, this study investigated the relationship between mindfulness and research creativity among 1210 Chinese graduate students. Additionally, we explored the mediating effect of flow experience and creative self-efficacy in this relationship. The research results showed that mindfulness had a direct positive effect on graduate students’ scientific research creativity. The mediating effect of flow experience and creative self-efficacy, as well as the chain mediating effect, were established, with the mediating ratio being 13.1% and 30.0%, respectively, and the indirect effect of chain mediating accounting for 34.1%. Interestingly, the effect mechanism at the gender level was various, with the mediating effect of mindfulness on scientific research creativity being higher among male graduate students. The results of this study revealed the mechanism of mindfulness on graduate students’ scientific research creativity, offering valuable insights for enhancing their creative capabilities in the realm of scientific research.