The present study investigated the parameters of nocturnal sleep that mediate the relationship between morningness-eveningness preference and the sleep architecture of naps in university students. This study had a cross-sectional, descriptive correlational design. The sleep architecture of 52 students invited to take an afternoon nap in the laboratory was recorded. The morningness-eveningness questionnaire (MEQ) was used to evaluate morningness-eveningness preference. An actigraph was used to collect students' nighttime sleep data in the week preceding the study. Polysomnography was used to measure the sleep architecture of the participants' naps. After adjustments for potential factors, although the MEQ did not directly correlate with the percentage of sleep stages in naps, the effects of the MEQ on the percentage of Stage 1 sleep, slow-wave sleep, and rapid eye movement sleep; sleep duration; and sleep efficiency of naps were mediated by the total sleep time in the preceding week. This preliminary study suggests that nap quality was affected by morningness-eveningness preference through the mediation of total nocturnal sleep time. Therefore, future studies should be carefully designed to consider nighttime sleep patterns when analyzing the effects of chronotypes on daytime sleep.