Previous research has shown that in prehigher education stages, inquiry-based teaching is not sufficient for forming a mature understanding of the nature of science (NOS). However, there is relatively little research conducted on colleges. Inquiry-based teaching should not overlook cognitive frameworks, as students' limited scientific reasoning abilities may become overwhelmed by the challenges of scientific inquiry. In the college physics laboratory, we manipulated underlying pedagogy (lecture, implicit inquiry, and explicit inquiry) and group compositions (homogeneous and heterogeneous), resulting in a 2 × 3 teaching treatments randomly across six classes (n = 208 students) to explore the effectiveness of different teaching methods and grouping strategies in enhancing college students' understanding of the NOS, as well as the potential relationship between students' views of the NOS and their scientific reasoning skills. This study found that students' understanding of the NOS was influenced by the teaching mode, and the teaching mode had different effects on students with varying abilities in scientific reasoning. Explicit inquiry-based teaching was particularly important for enhancing the understanding of the NOS among students with low to medium scientific reasoning abilities.