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In order to develop the strategy more suitable campus-based coronavirus disease 2019 (COVID-19) prevention programs for undergraduate students, it is critical to identify discrepancies in knowledge of COVID-19 prevention among students from different campuses in China. The present study examined the difference in preventive knowledge about COVID-19 pandemic in undergraduate students from two cities of Guangdong-Hong Kong-Macao Greater Bay Area (GBA), Macao Special Administrative Region (SAR), which had very few cases of COVID-19 patients, and Zhuhai, which is borders Macao SAR. In August 2020, two cohorts of undergraduate students from universities in Macao (n = 977) and Zhuhai (n = 2,818) were recruited for online. The self-rating questionnaire was used to gain information about their knowledge in COVID-19 prevention. Macao and Zhuhai students had similar correct rates in terms of heat inactivation conditions of SARS-CoV-2, (76.8% vs. 76.9%, P = 0.950), etiquette when coughing and sneezing (75.9% vs. 75.0%, P = 0.562), and use of disposable masks (92.2% vs. 90.6%, P = 0.126). However, students from Macao had significantly higher rates in correct use of disinfectants against SARS-CoV-2 (24.6% vs. 17.5%, P < 0.001) and in the route of transmission of SARS-CoV-2 (84.5% vs. 79.6%, P < 0.001) than those from Zhuhai. In conclusion, the knowledge level of COVID-19 prevention differs among undergraduate students from Macao and Zhuhai, which warrants an appropriate region-specific health education strategie for COVID-19 prevention. [ABSTRACT FROM AUTHOR]