This paper describes a scoping review of China's academic resource databases, relevant official websites, news reports and public accounts spanning a period from the end of 2019 to the end of 2022, to investigate the challenges in scientific integrity and ethical soundness of research conducted during and immediately after the COVID-19 pandemic in China. By conducting the scoping review with keywords related to the research questions in Chinese, relevant data were extracted and classified into four categories: challenges in research, challenges in ethics review, challenges in publishing academic work, and research ethics guidelines during and after the pandemic. The paper points out that problematic studies and findings increased with the escalation in medical research projects during the pandemic in China. The situation faced by researchers was more difficult than before the pandemic. The mode of informed consent, and ethics review and oversight systems also underwent changes. In addition, Traditional Chinese Medicine as an alternative medical treatment for COVID-19, attracted attention from the research community and became a topic of discussion. We conclude that the various challenges and concerns identified indicate a need for a proper and timely response system be formulated in preparation for possible future occurrences of new pandemics or other critical situations.