This study aimed to compare the changes in physical activity (PA), chronic disease, and mental health indicators of Koreans before and after the COVID-19 outbreak, using raw data from more than 400,000 representative samples from the 2019-2020 Community Health Survey by the Korea Centers for Disease Control and Prevention, and to explore the correlations among them. We used two-way ANOVA to analyze changes and differences in PA and obesity levels. We assessed the influence of gender and recurrent PA using chi-square tests for mental health status and chronic disease. Finally, we performed a correlation analysis to determine the relationships among PA days, mental health, and chronic disease. The results showed that, compared to the levels before the COVID-19 period, moderate-intensity (Days: 1.415~1.217; Time: 114.688~107.321) and high-intensity (Days: 0.798~0.671; Time: 112.866~106.110) PA significantly decreased in Koreans during the COVID-19 period, while low-intensity (Time: 60.305~61.735) PA increased. Before and during the COVID-19 period, men (18,436 (8.1%)~16,124 (7.0%)) performed PA more regularly than women (13,207 (5.8%)~9382 (4.1%)). Compared to the number of regular PA participants before the COVID-19 period, regular PA participants (male, female) decreased from 31,643 (13.8%) to 25,506 (11.1%) during the COVID-19 period. Compared with the levels before the COVID-19 period, the experience rates of stress (3.1%~2.6%), depression (0.8%~0.6%), HBP (3.0%~2.2%), and diabetes (1.2%~0.9%) significantly changed under different levels of conventional PA intervention. In addition, the obesity rate during the COVID-19 period (23.957) was higher than it was before COVID-19 (23.477). During the COVID-19 period, the PA of Koreans was greatly restricted, but low-intensity PA was maintained and increased. PA is an effective activity for maintaining mental health and for preventing and reducing chronic diseases. Recommendations for appropriate intensity or a combination of high-, moderate-, and low-intensity PA should be based on the health status of Koreans to help them maintain mental health and to reduce the risk of chronic diseases during COVID-19 social distancing.