Higher education plays an important role in preparing future citizens and leaders with the capacity to address systemic issues behind complex problems such as climate change. There have however been few attempts to assess systems-related competencies in the context of complex problems. This study adapted an existing scenario-based assessment tool to measure Taiwanese undergraduate students' systems thinking competency in the context of climate change. This tool included a climate-related problem scenario and eight follow-up prompts along with a scoring rubric. The scenario was set in a contextual setting familiar to students in Taiwan. Using this tool and an additional knowledge survey, we investigated undergraduate students' (N = 110) systems thinking competency and its relationship to their content knowledge, and further examined the effect of an interdisciplinary climate change course on students' systems thinking and content knowledge. Data analysis revealed a modest level of systems thinking competency among the students, and a significant, positive association between the competency level and content knowledge. Participating in the semester-long course positively influenced student learning outcomes. However, the effect was focused on STEM students. These results provide important implications for teaching and learning of systems thinking competency in the context of complex issues.