Although some studies showed that lifestyle was associated with oral health behavior, few studies investigated the association between household type and oral health behavior. The aim of this prospective cohort study was to investigate the association between household type, oral health behavior, and periodontal status among Japanese university students. Data were obtained from 377 students who received oral examinations and self-questionnaires in 2016 and 2019. We assessed periodontal status using the percentage of bleeding on probing (%BOP), probing pocket depth, oral hygiene status, oral health behaviors, and related factors. We used structural equation modeling to determine the association between household type, oral health behaviors, gingivitis, and periodontitis. At follow-up, 252 students did not live with their families. The mean ± standard deviation of %BOP was 35.5 ± 24.7 at baseline and 32.1 ± 25.3 at follow-up. In the final model, students living with their families were significantly more likely to receive regular dental checkup than those living alone. Regular checkup affected the decrease in calculus. The decrease in calculus affected the decrease in %BOP over 3 years. Living with family was directly associated with regular dental checkups and indirectly contributed to gingival status among Japanese university students.