Recently, the microbiota-gut-brain axis (MGBA) has emerged as a target for therapeutic innovation. Impairment of dynamic relationships within the MGBA promotes the pathological features of metabolic diseases. However, experimental data on the MGBA has limited clinical application. This review summarizes recent studies and proposes that exploring the interaction among peripheral organs and the MGBA could verify the dominant role of the latter in the onset of metabolic diseases and promote the clinical application of research outcomes. We first emphasize the molecular basis of metabolic diseases caused by MGBA disorders, which manifests as bidirectional relationship. We also summarize related therapeutic strategies, along with limitations in their clinical application. Adipose tissue (AT) is dynamic during metabolic activities and might interact with components in the MGBA. Therefore, it is interesting to explore the interplay among the MGBA and different kinds of AT, including thermogenic adipose tissue and white adipose tissue (WAT). In addition, we also evaluate the functional specificity of adipose tissue derived mesenchymal stem cells (ADSCs) and the beige adipose tissue. Understanding the heterogeneity and molecular basis of the interaction between different kinds of AT and the MGBA could accelerate innovation in the diagnosis and therapy of metabolic diseases.