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This study aims to develop an instrument to assess and analyze student’s systems thinking skills in the context of the COVID-19 pandemic. Students answered questions about six systems of varying complexity relevant to the COVID-19 pandemic. Questions were designed to elicit student understanding of the system’s organization, system’s behavior, and student’s ability to manipulate the system to achieve desired goals. The instrument was administered to 2794 high school students in two provinces in China with additional items to collect background information. M-regression analysis revealed that age, internet use time on weekends, and life satisfaction were the most influential predictive variables for systems thinking. Additionally, significant differences in family members and communication resources exist between high, middle, and low scoring groups.