Inquiry-based practices have important impacts on student science learning outcomes, yet the psychological mechanisms behind the relationships are less clear. This study aimed to explore the mediating effects of science attitudes in the relationship between student-perceived inquiry-based practices and scientific literacy using data from eight countries in the 2015 Programme for International Student Assessment (PISA). Results of multilevel structural equation modeling (MSEM) suggested that (1) the three science attitudinal factors, i.e., interest in science, science self-efficacy, and instrumental motivation of learning science, served as significant mediators between perceived inquiry-based practices and scientific literacy; (2) the direct effect of perceived inquiry-based practices on scientific literacy was consistently negative across the countries, yet consistently positive on the three attitudinal factors; and (3) the indirect effects of perceived inquiry-based practices on scientific literacy via interest in science and science self-efficacy were consistently positive across the countries while negative via instrumental motivation for six out of the eight countries. The results may provide deeper insights into inquiry-based practices and suggest ways for science educators to improve student science attitudes and science learning outcomes.