The research described in this paper investigated science students’ perceptions of their university learning environments and associations of these perceptions with their academic engagement and satisfaction. Data were collected from 1,169 junior students majoring in science from 17 universities in Taiwan. The quantitative research incorporated factor analysis, higher order factor structure, and hierarchical multiple regression analyses. The results revealed science students’ diverse views of various environmental aspects and identified key aspects influencing the outcome measures, after controlling for student background and institutional characteristics. Faculty-student relation was the aspect that most strongly affected both academic engagement and learning satisfaction of these science students. Perceived adequacy of library resources, student services, enhancement of science capacities and language abilities, and relations with faculty were all positively related to the overall satisfaction of science students with their universities. By exploring potential influences of academic environment, the study contributes to a better understanding of the nature and intricate impact of the learning environment on the performance of undergraduate science majors in Taiwan and the need for reflection and improvement.