This study explored the effects of congruency between preferred and actual learning environment (PLE & ALE) perceptions on students' science literacy in terms of science concepts, attitudes toward science, and the understanding of the nature of science in an innovative curriculum of High Scope Project, namely Sci-Tech Mind and Humane Heart (STMHH). A pre-/post-treatment experiment was conducted with 34 Taiwanese tenth graders involved in this study. Participating students' preferred learning environment perception and pre-instruction scientific literacy were evaluated before the STMHH curriculum. Their perceptions toward the actual STMHH learning environment and post-instruction scientific literacy were also examined after the STMHH. Students were categorized into two groups; "preferred alignment with actual learning environment" (PAA) and "preferred discordant with actual learning environment" (PDA), according to their PLEI and ALEI scores. The results of this study revealed that most of the students in this study preferred learning in a classroom environment where student-centered and teacher-centered learning environments coexisted. Furthermore, the ANCOVA analysis showed marginally statistically significant difference between groups in terms of students' post-test scores on scientific literacy with the students' pre-test scores as the covariate. As a pilot study with a small sample size aiming to probe the research direction of this problem, the result of marginally statistically significant and approaching large sized effect magnitude is likely to implicate that the congruency between preferred and actual learning environments on students' scientific literacy is noteworthy. Future study of this nature appears to merit further replications and investigations.