Parent-child separation caused by parental migration could have adverse effects on individuals’ emotional adaptation. However, research on this topic is limited in its focus on childhood or adolescence samples and solely environmental factors, and less is known about how positive environmental factors, biological factors and parent-child separation experience interact to influence emotional adaptation in emerging adulthood. The present study addressed these issues by investigating the relationships between parent-child cohesion and positive/negative affect, and examining the moderating roles of sympathetic nervous system activity (measured by skin conductance level reactivity, SCLR) and parent-child separation experience in the relationships. Data from 248 college students (Mage = 18.91 years, SD = 0.70; 32.3% males), including 158 college students with parent-child separation experience and 90 college students without parent-child separation experience. The results showed that parent-child cohesion predicted college students’ positive/negative affect. Moreover, the moderating role of SCLR on the relationship between father-child cohesion and negative affect varied with parent-child separation experience. Specifically, father-child cohesion negatively predicted negative affect when SCLR was lower for college students with parent-child separation experience, while negatively predicted negative affect when SCLR was higher for college students without parent-child separation experience. These results indicate that the interaction pattern of Biological × Environmental predicting college students’ positive/negative affect varies across parent-child separation status in childhood or adolescence.