Objective: To investigate the variability of the time and frequency of Moderate to Vigorous Physical Activity (MVPA) during the school days and weekends of junior high school students, and to explore the correlation between MVPA and physical fitness. Methods: A cluster sampling method was used to investigate 79 students of grade 1 and grade 2 in Beijing Huilongguan Middle School. Adapted one day physical activity recording tool was implemented to investigate students’ physical activity from 8:00 to 23:00 a week, activity records were classified into daily MVPA parts and non MVPA parts based on MET values. Physical activity time series for 5 consecutive days and 2 weekends, as well as MVPA total time and the lempel ziv complexity of the sequence was calculated. Investigated the correlation between the MVPA situation and the results of national students’ physical fitness standard test. Results: There was no statistical difference in MVPA time between males and females during school days( t =-0.90, P >0.05). Females had greater variability in MVPA than males(58.9%, 53.5%). There was also no statistical difference in MVPA complexity between genders( t =-0.55, P >0.05). During weekends, there was no significant difference in the total MVPA time between men and women( t =-0.13, P >0.05). The CV of male MVPA time was lower than that of female(141.5%, 152.8%). There was also no significant difference( t =-0.63, P >0.05), and male MVPA complex CV was slightly higher than that of female ( 55.1% , 48.1%). The MVPA time CV of adolescents during weekdays was slightly lower for males (weekdays vs weekends: 53.5%, 141.5%) than females(58.9%, 152.8%). The MVPA complexity in weekdays among males was moderately correlated with BMI( r =0.41), and the MVPA time and weight of females ( r =-0.30) and BMI ( r =-0.31) were low. The complexity was related to body weight ( r =-0.31) and BMI ( r =-0.33) to a low degree( P <0.05). Conclusion Junior middle school students are more active on school days than weekend, but the MVPA time series are limited. Schools can effectively improve physical fitness by spreading out the activity period of MVPA in one day. MVPA complexity, as a more comprehensive indicator, may be more sensitive to BMI of junior middle school students.