Two major perspectives have guided theory and research into student learning in higher education: Students’ perceptions of the learning environment and student engagement. As literature suggests, students’ perceptions of the learning environment and engagement can significantly predict their learning. These studies, however, were conducted separately, and researchers have not examined the joint effects of perceptions of the learning environment and engagement on learning. The present study thus attempted to examine the relationships among Chinese undergraduates’ perceptions of the learning environment, engagement, and three types of learning outcomes. The mediating effects of student engagement on the relationship between perceptions of the learning environment and outcomes were expected. A sample of 3,063 sophomores from a full-time research-oriented university in Mainland China were surveyed through an online questionnaire platform. Convenience sampling was used to choose the respondents. Presage, process, and product variables were measured in the study. The presage variables included course experience and cocurricular experience. The process variable referred to student engagement. The product variables were measured by learning outcomes of academic achievement, generic skills, and learning satisfaction. CFA was performed to assess the construct validity of the measures. SEM was used to examine the relationships among variables, as well as to test the mediating effects of engagement on the relationship between presage variables and learning outcomes. The CFA results showed that the measures were reliable and valid in assessing Chinese undergraduate’s perceptions of their learning environment, engagement, and learning outcomes. The SEM results supported a model which showed that students’ perceptions of the learning environment had a direct effect on learning outcomes and an indirect effect, via their engagement: (1) Student engagement partially mediated the relationship between perceptions of the learning environment and academic achievement, (2) student engagement fully mediated the relationship between perceptions of the learning environment and generic skills, and (3) student engagement partially mediated the relationship between perceptions of the learning environment and learning satisfaction. The results confirmed the benefits of perceptions of the learning environment and student engagement on learning. As expected, student engagement has an effect on learning, and the engagement is in turn predicted by perceptions of the learning environment. Students’ perceptions of the learning environment can also directly predict their GPA and satisfaction. Based on the results, university should try to create a positive learning environment to improve students’ learning experience, and to increase their engagement. Resources are suggested to be placed on these educational experiences outside the classroom to achieve a quality undergraduate education. The curriculum should be structured to induce students to devote more time and effort to academic related activities. Teachers should attach great importance to teaching quality and improve their instructional design, including well organizing their lessons, providing clear teaching objectives and requirements, encouraging discussion and reflective thinking, as well as offering guidance and freedom of study. Students’ ability and satisfaction can thus be promoted by improving their in-class and out-of-class learning experience, and by increasing learning engagement. Limitations and direction for future research are discussed in the end.