Introduction: This study aims to investigate how mother-adolescent relationships evolved before and during the COVID-19 pandemic and their correlation with pandemic-related stress and adolescents' psychological distress. Methods: A longitudinal study involving 579 mother-adolescent dyads (junior high school students at Time 1; 50% male students) was conducted, with data collected before (October 2019) and during (October 2020) the pandemic in Japan. Both mothers and adolescents reported the perceived quality of their positive and conflictual relationships at each time point. At Time 2, assessments were made regarding perceived pandemic-related stress and adolescent psychological distress. Results: Structural equation modeling, cross-lagged regression, and mediation analysis revealed that perceptions of relationships by both mothers and adolescents before the pandemic predicted and sustained their own and their partners' perceptions during the pandemic. Furthermore, adolescents' perceptions of positive relationships with mothers protected against adolescents' distress. Otherwise, their perceptions of conflictual relationships with mothers posed a risk for adolescents' psychological distress. Additionally, the maintenance of adolescents' higher perception of positive relationships with their mothers was mediated by their perceived higher pandemic-related stress. Conclusions: These findings underscore the reciprocal and additive nature of mothers' and adolescents' perceptions of relationship quality, which in turn predict adolescents' mental health during stressful situations like a pandemic. Moreover, adolescents are encouraged not to suppress negative feelings about stress, to enhance perceptions of a positive relationship perceptions with their mother.