Short sleep is a common issue nowadays. The purpose of this study was to investigate prefrontal cortical hemodynamics by evaluating changes in concentrations of oxygenated hemoglobin (HbO) in cognitive tests among short-sleep young adults and to explore the relationship between sleep duration, physical activity level, and cognitive function in this specific population. A total of 46 participants (25 males and 21 females) were included in our study, and among them, the average sleep duration was 358 min/day. Stroop performance in the short sleep population was linked to higher levels cortical activation in distinct parts of the left middle frontal gyrus. This study found that moderate-to-vigorous physical activity (MVPA) was significantly associated with lower accuracy of incongruent Stroop test. The dose-response relationship between sleep duration and Stroop performance under different levels of light-intensity physical activity (LPA) and MVPA was further explored, and increasing sleep time for different PA level was associated with better Stroop performance. In summary, this present study provided neurobehavioral evidence between cortical hemodynamics and cognitive function in the short sleep population. Furthermore, our findings indicated that, in younger adults with short sleep, more MVPA was associated with worse cognitive performance. Short sleep young adults should increase sleep time, rather than more MVPA, to achieve better cognitive function.