Objective To explore the relation between stigma and substance use of patients with substance use disorder and explore the impact of learning addiction medicine massive open online course (MOOC) on patients’ stigma, depression and anxiety. Methods Patients with substance use disorder in Meishan Detoxification Center from January 11 to 18, 2020 were selected. The patients were randomly divided into control group and teaching group. Both groups participated in regular labor reform while the teaching group attended extra MOOC course. The general demographic data and the duration and amount of substance use were collected before intervention. Before and after intervention, all the patients completed scales including Chinese Version of Substance Use Stigma Mechanisms Scale (SUSMS-C), Zung Self-Rating Depression Scale (SDS) and Zung Self-Rating Anxiety Scale (SAS). The correlation between stigma and depression, anxiety, substance use characteristics were analyzed, as well as the changes of stigma, depression and anxiety before and after MOOC intervention.Results A total of 78 patients were included, including 41 in the control group and 37 in the teaching group. There was no correlation between the scores of SUSMS-C and the duration or amount of substances use (P>0.05). SAS score and SDS score were positively correlated with the total score of stigma, internalized stigma, enacted stigma (family) and enacted stigma (healthcare providers) (P<0.05). SDS scores and SAS scores had no correlation with the anticipated stigma (P>0.05). After intervention, the total score of stigma, anticipated stigma (family) and anticipated stigma (healthcare providers) in the teaching group decreased (P<0.05). In the control group, only anticipated stigma (family) decreased (P=0.047). There was no significant difference in other SUSMS-C items, SAS scores, or SDS scores between the two groups before and after intervention (P>0.05). Conclusions Stigma may not be able to protect patients with substance use disorder from using substances. Instead, stigma may potentially cause negative emotional consequences like depression and anxiety. The addiction medicine MOOC can be used as an intervention to reduce the stigma of patients with substance use disorder.