This article systematically compares the multiple mechanisms by which laparoscopic sleeve gastrectomy (LSG) and Roux-en-Y gastric bypass (RYGB) affect postoperative metabolism in obese patients with obstructive sleep apnea (OSAS). As a key comorbidity of OSAS, gastroesophageal reflux disease (GERD) has a bidirectional pathological exacerbation relationship with OSAS, and the different effects of these two procedures on GERD are directly related to the postoperative remission of OSAS. In addition to reducing upper airway fat deposition and alleviating intermittent hypoxia and systemic inflammation through weight-dependent mechanisms, both procedures directly regulate glucose and lipid metabolism via non-weight-dependent mechanisms such as gastrointestinal hormone remodeling, bile acid signal activation, and gut microbiota regulation. Among them, RYGB shows superior advantages in the regulation of enteric hormones and bile acids, and has a definite anti-reflux effect; while LSG exerts metabolic benefits by strongly inhibiting ghrelin and enhancing GLP-1/PYY responses, and can also inhibit oxidative stress-induced adipose inflammation through regulating the GLP-1/DPP-4 pathway, but carries the risk of inducing or exacerbating GERD. This review aims to provide a comprehensive mechanistic basis for the individualized selection of surgical procedures for obese patients with OSAS, especially those with concomitant GERD.