The number of mothers suffering from mental illness is increasing steadily, particularly under conditions of the coronavirus disease pandemic. The identification of factors that contribute to resilience in mothers is urgently needed to decrease the risks of poor physical and psychological functioning. We focused on the risk of parenting stress and psychological resilience in nonclinical mothers and conducted two studies to examine the relationships between intestinal microbiota, physical condition, and psychological state. Our results showed that alpha diversity and beta diversity of the microbiome are related to high parenting stress risk. Psychological resilience and physical conditions were associated with relative abundances of the genera Blautia, Clostridium, and Eggerthella. This study helps further understand the gut–brain axis mechanisms and supports proposals for enhancing resilience in mothers.