Background: Since the end of 2019, the COVID-19 pandemic has had serious wide-ranging effects on academic, occupational and other daily activities. Like other types of institutions, schools are facing unprecedented challenges. Students may face a variety of adverse consequences, including sleep disturbances and school bullying, if they are unable to adjust to the current learning and living environment. This study explored the effects of the COVID-19 pandemic on school bullying. Methods: A total of 5782 middle school students were enrolled in this multi-stage, cross-sectional study (3071 before and 2711 during the pandemic). The pre-pandemic group had a mean age of 14.9 ± 1.73, the pandemic group of 14.75 ± 1.47. Three models were set up using binary logistic regression to adjust for confounding variables (gender, school type, alcohol consumption, smoking, playing violent video games). Results: All types of bullying victimization and perpetration (physical, verbal, social and property bullying) were more common during the pandemic than before the pandemic. In terms of bullying victimization, property bullying victimization (crude odds ratio [OR]: 2.398, 95% CI: 2.014–2.854, p < 0.001; model 2 adjusted OR: 2.344, 95% CI: 1.966–2.795, p < 0.001; model 3 adjusted OR: 2.818, 95% CI: 2.292–3.464, p < 0.001) increased the most. In terms of bullying perpetration, verbal bullying perpetration (crude OR: 3.007, 95% CI: 2.448–3.693, p <0.001; model 2 adjusted OR: 2.954, 95% CI: 2.399–3.637, p < 0.001; model 3 adjusted OR:3.345, 95% CI: 2.703–4.139, p < 0.001) increased the most. Conclusion: This study corroborate the significance of the pandemic on traditional school bullying and suggests that we should further consider other types of bullying and establish and improve the response and prevention mechanisms during public health emergencies such as the COVID-19 pandemic.