Objectives The shortage of emergency drugs in China is severe. This study aimed to characterize emergency drug shortages in China and to measure their effects. Methods An online questionnaire based on a literature review was sent to emergency department physicians in Chinese secondary and tertiary hospitals from November 2016 to February 2017. The survey asked physicians questions about their experiences with emergency drug shortages. Results In total, 236 physicians from 29 provinces participated in the survey. According to their responses, 90.7% of the respondents experienced drug shortages during the last year. More than half of the physicians (65.7%) reported that drug shortages occurred at least once a month. Hospitals in the eastern and western regions of China had more emergency drugs in shortage than hospitals in central China, especially those with many inpatient beds (≥800). In addition, the shortage situation was more serious in secondary hospitals than in tertiary hospitals. More respondents agreed that original medicines, injections, essential medicines, medicines without alternative agents and cheap medicines were more susceptible to shortages than generics, oral medicines, nonessential medicines, medicines with alternative agents and expensive medicines, respectively. Most respondents thought that drug shortages always, often or sometimes affected patients [delayed therapy (62.6%), longer rescue and recovery times (58.9%) and higher costs (58.7%)] and physicians [inconvenience (81.0%), higher pressure (76.5%) and harm to patient-doctor relationships (72%)] and compromised hospital reputations (55.1%). Conclusions The shortage of emergency drugs in China is serious, especially in secondary hospitals located in eastern and western China. Emergency drug shortages have significant effects on patients and physicians.