The COVID-19 epidemic adversely affects the lifestyle of people. This study aimed to examine the impacts of social isolation on physical activity (PA) levels and mood states of children and adolescents and to explore the correlation between them during the COVID-19 epidemic. A total of 9979 children and adolescents (11.63 ± 1.23 years old) from Yan'an, China volunteered to participate in this study and completed online questionnaires. PA and mood states were measured by International Physical Activity Questionnaire Short Form (IPAQ-SF) and Profile of Mood States (POMS), respectively. The results showed that the mean of students' moderate-to-vigorous PA (MVPA) was 23.19 min per day. The total mood disturbance in the moderate and high-level PA groups were significantly lower than those in the low-level PA group ( < 0.05). Additionally, boys and girls had significant differences in PA levels ( < 0.01), and the PA levels of students in different grades were also significantly different ( < 0.01). Meanwhile, boys' mood states were worse than girls'. The Grade 4 in primary schools had the worst mood states while Grade 5 had the best mood states. The results suggested that the MVPA of students has dropped badly, compared with the results of previous studies investigated in normal times. In addition, the PA level had a significantly positive impact on the mood states of children and adolescents during the COVID-19 epidemic. Sex and grades were factors which affected the PA levels and mood states. This study can help policymakers and healthcare professionals understand PA and mood states of Chinese children and adolescents during the epidemic. We should pay attention to the changes in PA levels and mood states of children and adolescents.