Previous studies have examined the moderating effect of respiratory sinus arrhythmia (RSA) on the association between marital conflict and externalizing problems, however the findings were inconsistent. One possible reason is that the covariation of internalizing problems in externalizing problems. Therefore, the present study aimed to examine this issue. Participants were 332 Chinese adolescents (54.5% boys) age from 13 to 15 years old. At T1, electrocardiogram monitoring was performed on adolescents during the resting state and stressor tasks (a speech task and a mental arithmetic task) to obtain RSA data. The Chinese version of the Achenbach Youth Self-Report-2001 (YSR-2001) and the Chinese version of the Children’s Perception of Interparental Conflict scale were used to assess adolescents’ externalizing and internalizing problems and their perception of marital conflict, respectively. Adolescents’ problem behaviors were assessed again in the second and third waves of data collection, with a 1-year lag among each wave. The results revealed that the 3- interactions of marital conflict × RSA reactivity in speech task × sex significantly predicted the trajectory of externalizing problems when controlling for internalizing problems from externalizing problems. Specifically, girls with greater RSA suppression to the speech task reported low and stable externalizing problems, however, boys with the same pattern were associated with slightly increased levels of externalizing problems. While, RSA augmentation to the speech task predicted the increase in externalizing problems among both girls and boys in high marital conflict families over time. However, this interaction effects were not significant when not partial out internalizing problems from externalizing problems. The findings highlight the importance of controlling for the covariation of internalizing problems when examining the interaction effects of person and environment on the development of adolescents’ externalizing problems.