Bariatric surgery has been the first-line treatment for obesity. Since the 2010s, gradual changes in miRNAs upon surgery have been observed. Substantial research has been undertaken on the role of bariatric surgery in the gastrointestinal tract. However, bariatric surgery research largely ignores the role of miRNAs in organs other than the gastrointestinal tract, while the contribution of miRNAs to this process has received little attention. This review addresses a neglected aspect of miRNAs in obese patients undergoing bariatric surgery, especially the obvious effect on multisystem organs. This finding provides evidence that miRNAs play a complex yet important role in the functional stability of each organ and the weight loss efficacy after bariatric surgery. The results provide a solid evidence base for the mechanism of bariatric surgery. Taking into account incompatible medication adherence associated with adverse outcomes, suggestions were identified for an efficient technical refinement of bariatric surgery with better clinical results.