Background Menstruation affects the physiological and psychological health of East Asian women, imposing burdens on their daily lives and work. The gut microbiota has been found to improve various diseases. The study used Mendelian randomization to exploratorily discuss the causal effects of gut microbiota on the menstruation quality of life impacts. Methods According to the predefined threshold, independent genetic variants significantly linked to 119 bacterial genera in the gut were extracted as instrumental variables. The inverse variance weighted (IVW) was utilized as the primary analysis method, supplemented by MR-Egger and Weighted median methods. Effect estimates were assessed primarily using the odds ratios (OR) and 95% confidence intervals (95%CI). In addition, sensitivity analyses (heterogeneity, horizontal pleiotropy, and outliers) were implemented to evaluate the robustness and accuracy of the findings. Results Causal effects were found between 28 bacterial genera and 13 menstruation quality of life impacts. Based on OR, 18 bacterial genera were identified as risk factors, while 10 were identified as protective factors. Furthermore, sensitivity analysis did not detect heterogeneity, horizontal pleiotropy, or outliers. Conclusions This study provides evidence for causal effects of gut microbiota on menstruation quality of life impacts. These findings will help elucidate how gut microbiota could affect physiological and psychological health issues during menstruation. Furthermore, they also offer valuable perspectives into the management of women's health during menstruation.