Few studies have examined relationships among neurophysiological, psychological, and behavioral factors with regard to their effects on sleep quality. We used a structure equation model to investigate behavioral and psychological factors that influence neurophysiological regulation of sleep in shift workers. Using a cross-sectional study design, we tested the model with a sample of 338 female nurses working rotating shifts at an urban regional hospital. The Morningness-Eveningness Questionnaire (MEQ) and short-form Menstrual Distress Questionnaire (MDQ) were used to measure neurophysiological factors involved in morningness-eveningness and menstrual distress. The Sleep Hygiene Awareness and Practice Scale (SHAPS) and Profile of Mood States Short Form (POMS-SF) were completed to measure behavioral factors of sleep hygiene practices and psychological factors of mood states. In addition, the Pittsburgh Sleep Quality Index (PSQI) measured participant's self-reported sleep quality. The results revealed that sleep hygiene practices and mood states mediated the effects of morningness-eveningness and menstrual distress on sleep quality. Our findings provide support for developing interventions to enhance sleep hygiene and maintain positive mood states to reduce the influence of neurophysiological factors on sleep quality among shift workers.