This study aims to examine influence paths of three metacognitive reading strategies (metacognitive understanding and remembering strategies, metacognitive summarizing strategies and metacognitive assessing credibility strategies) on scientific literacy, mediated by reading self-efficacy and reading literacy. The dataset included 11,420 15-year-old students from four Chinese provinces (Beijing, Shanghai, Jiangsu and Zhejiang) who took part in the Programme for International Student Assessment (PISA) in 2018. The results of structural equation model showed that metacognitive assessing credibility strategies had the greatest effect on the scientific literacy, and reading literacy played an important mediating role in the relationship between the three metacognitive reading strategies and scientific literacy. The results of the multi-group structural equation model indicated that there were significant differences in influence pathways between boys and girls, and that the reading self-efficacy of boys and girls played a different role in the impact of metacognitive summarizing strategies on scientific literacy. This study reveals the mechanism and gender difference of metacognitive reading strategies on the scientific literacy.