In 2019, Taiwan’s Ministry of Education introduced 12-Year Basic Education, aiming to enhance students’ reading literacy skills. Experts stressed the importance of reading for problem-solving and cross-disciplinary understanding. Teachers aimed to teach diverse reading strategies. This study explored the relationship between metacognition and reading literacy in Taiwan, using PISA 2009 and 2018 data. The analysis used hierarchical linear modeling to account for nested influences of students and schools. Gender and ESCS were considered to assess the educational reform’s impact. Results showed: (1)Reading skills improved in Taiwan over the past decade, especially for ninth graders. (2)Metacognitive abilities in reading were still below OECD averages, notably in Understanding and Remembering strategies. (3)Gender differences in metacognition grew. (4)The ICC value decreased significantly for tenth graders. (5)ESCS-based reading performance gap widened between the highest and lowest quartiles. Therefore, nurturing metacognition is crucial for enhancing reading literacy.