The global prevalence of obesity and its associated metabolic disorders keeps rising, presenting a major challenge to public health. The gut microbiota plays a pivotal role in obesity onset and development, and its dysbiosis and dysfunction are closely associated with obesity and its complications. This review synthesizes the pathological mechanisms underlying the heredity, neuroendocrine, chronic inflammation, and the gut microbiota-metabolism axis of obesity. Then, we explore the positive and negative regulatory effects of opportunistic pathogens (e.g., Desulfovibrio spp., Megamonas spp.) and putative beneficial bacteria (e.g., Lactobacillus spp., Akkermansia muciniphila) on obesity. Furthermore, we summarize the mechanisms by which these signature gut microbes drive the development of obesity-related conditions, including type 2 diabetes mellitus, metabolic dysfunction-associated steatotic liver disease, cardiovascular diseases, and hypertension. We firstly propose a gut microbiota trajectory hypothesis to delineate the interrelationships between these representative gut microbial signatures and the onset and progression of obesity and its complications. Finally, the review discusses future research directions and the potential for developing early diagnostic technologies based on these microbial signatures. Collectively, this work aims to provide novel strategies for the early diagnosis and precision intervention of obesity and related metabolic disorders, thereby advancing the development of personalized therapeutics.