The main aim of this study was to explore the association between overweight/obesity and executive control (EC) in young adults, and to further analyze the mediating effect of brain-derived neurotrophic factor (BDNF) and serotonin (5-hydroxytryptamine (5-HT)) on the relationship between overweight/obesity and EC. A total of 449 college students aged between 18 and 20 years were recruited for the study between March and December 2019. Their height and weight were then measured professionally. Subsequently, body mass index (BMI) was calculated as weight (kg) divided by the square of height (m). The EC of the participants was then estimated using the Flanker task, while their serum BDNF levels and 5-HT levels were measured using an enzyme-linked immunosorbent assay (ELISA) kit. Finally, the multiple intermediary models in SPSS were used to analyze the mediating effect of 5-HT and BDNF between overweight/obesity and EC. The result show that the overweight/obesity of college students was positively correlated with the response of EC (p ≤ 0.005). However, it was negatively correlated with BDNF (p ≤ 0.05) and 5-HT (p ≤ 0.05). Moreover, BDNF (p ≤ 0.001) and 5-HT (p ≤ 0.001) were negatively correlated with the response of EC. The BDNF level played a partial mediating role between overweight/obesity and EC that accounted for 7.30% of the total effect value. Similarly, the 5-HT of college students played a partial mediating role between overweight/obesity and EC that accounted for 8.76% of the total effect value. Gender and age had no regulatory effect on the relationship between overweight/obesity, BDNF, 5-HT, and EC. This study provides the evidence that 5-HT and BDNF mediated the association between overweight/obesity and executive control. It is indicated that 5-HT and BDNF might be the biological pathways underpinning the link between overweight/obesity and executive control.