Global childhood and adolescent obesity has become a pressing public health challenge, imposing significant burdens on human health. Obesity is an independent risk factor for insulin resistance, which in turn serves as a critical initiating event for multiple chronic metabolic diseases. The Developmental Origins of Health and Disease (DOHaD) theory highlights the existence of a plastic ^”window period^” during early life, spanning pregnancy and lactation. Maternal nutritional status during this window period profoundly influences offspring metabolic health, with intergenerational transmission of gut microbiota acting as a key mediating pathway. This review summarizes current evidence on how maternal nutrition during the ^”window period^” shapes maternal and offspring gut microbial ecosystems and explores the relationship between these alterations and metabolic risks of obesity and other metabolic disorders in offspring. Based on emerging research, it has been found that maternal nutritional intake during this critical window period modulates early colonization of offspring gut microbiota through multiple pathways, thereby programming long-term metabolic trajectories. These findings suggest that targeting gut microbiota as a preventive strategy during the ^“window period^” may offer novel approaches for combating metabolic disorders, while also providing mechanistic insights into potential microbiota-modulating interventions. This perspective could inform future research directions and clinical applications in metabolic disease prevention.