Introduction Studies have suggested that the vaginal microbiome and gut microbiome are involved in pregnancy-related diseases, but little exploration of the link with early miscarriage or threatened miscarriage (TM) has been done. Whether the characteristics of the vaginal microbiome and gut microbiome in early pregnancy are related to TM and early pregnancy outcomes remains unclear. Methods and analysis The Microbiome Characteristics in Early Threatened Miscarriage Study (MCETMS) is a prospective investigation that will recruit 326 pregnant women with early TM. Pregnant women will be enrolled at 4-8 weeks of gestation, and their vaginal secretions, faecal samples, clinical data and sociodemographic characteristics will be collected prospectively. Pregnant women with TM will be followed up to 12 weeks of gestation to determine the early pregnancy outcomes (ongoing pregnancy or pregnancy loss). DNA will be extracted from the collected samples and will be analysed by 16S rRNA gene sequencing. Ethics and dissemination The MCETMS study protocol has been approved by the Ethics Committee of the First Affiliated Hospital of Guangzhou Traditional Chinese Medical University (ZYYECK[2020]051). Dissemination of study findings will occur through peer-reviewed journals, conferences and presentations.