Background: A good classroom environment can promote students' learning motivation and affect their academic efficacy and adaptation. This study compares the perceptions of Taiwanese middle school students regarding actual and preferred classroom environments and explores the association with sex and grade level. Methods: Data were collected using cross-sectional research design from a national sample of 1932 middle school students. Data of 1897 valid questionnaires from the Chinese Elementary and Middle School Inventory of Classroom Environment were analyzed. Results: The actual and preferred classroom environments perceived by students differed significantly (p?<?0.001). The overall mean score of actual classroom environment was lower than that of preferred classroom environment. Differences between the actual and preferred environments were greater for girls than for boys (p?<?0.001). Moreover, girls had higher scores than those of boys for both actual (p?=?0.036) and preferred (p?<?0.001) environments. After adjusted for region, seventh- and eighth-grade students had a higher score than that of ninth-grade students on preferred classroom environment (p?=?0.002). Conclusions: This study identified a gap between the ideal and actual classroom environments. We suggest that the government, schools, and health education teachers improve classroom environments during school health programs to satisfy students' expectations and thus increase their learning efficacy and overall well-being.