The purpose of this study was to explore the differences between the prevalence and impact factors of adolescent dissociative symptoms (ADSs) by using sex-stratification during the coronavirus disease 2019 (COVID-19) pandemic. A school-based, two-center cross-sectional study was conducted in Hangzhou City, China, between January 1, 2021 and April 30, 2022. The sample included 1,916 adolescents aged 13–18 years that were randomly selected using a multiphase, stratified, cluster sampling technique. A two-stage assessment procedure was used to find out the ADSs. We used a multivariate logistic regression analysis to assess the impact factors of ADSs during the COVID-19 pandemic. The adolescent dissociative scores (t = 4.88, P < 0.001) and positive ADSs rate (Chi-square = 15.76, P < 0.001) in males were higher than in females. Gender-stratified, stepwise multiple logistic regression analysis revealed that the conflict relationship of teacher-student [adjusted odds ratio (AOR) 1.06, 95% confidence interval (CI) 1.01–1.10], family expressiveness (AOR 0.87, 95% CI 0.78–0.98), family conflict (AOR 1.15, 95% CI 1.05–1.27), family organization (AOR 0.88, 95% CI 0.78–0.99), and family cohesion (AOR 0.87, 95% CI 0.77–0.99) were linked to ADSs only in males, while individual psychological states of somatic complaint (AOR 1.04, 95% CI 1.00–1.08) and paranoid ideation (AOR 1.09, 95% CI 1.01–1.19) were associated with female ADSs only. The ADSs seemed to be prevalent in Hangzhou City, studied during the COVID-19 pandemic. Gender differences in the prevalence and impact factors of dissociative symptoms seem to be significant among adolescents. Thus, gender-specific intervention programs against ADSs should be considered as reducing this risk.