Some cases of halitosis associated with small intestinal bacterial overgrowth (SIBO) are refractory to antibiotic therapy. The low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) diet (LFD) has emerged as an alternative therapeutic option for SIBO. This retrospective study is the first to investigate the efficacy of LFD in refractory SIBO-associated halitosis. We consecutively reviewed data from 141 patients with refractory SIBO-associated halitosis who underwent a four-week LFD intervention. Halitosis was diagnosed using organoleptic test. Volatile sulfur compounds—including hydrogen sulfide, methyl mercaptan (MM) and dimethyl sulfide (DMS)—were quantified in nasal breath using the OralChroma device. SIBO was confirmed via hydrogen/methane breath test. Serum nutritional parameters were measured to assess nutritional status. Dietary adherence was evaluated using the FODMAP Adherence Report Scale. All patients demonstrated good adherence to the LFD, with no significant changes in nutritional parameters post-treatment. Overall, 80.85% and 78.72% of the patients exhibited SIBO resolution and halitosis improvement, respectively. DMS levels significantly decreased after treatment [41.84 ± 10.73 parts per billion (ppb) vs. 19.22 ± 7.91 ppb, P < 0.001]. In contrast, baseline hydrogen sulfide (17.08 ± 12.30 ppb) and MM (13.50 ± 5.65 ppb) levels were low and remained unchanged post-treatment (P > 0.05). Moreover, post-treatment comparison between SIBO-negative and SIBO-positive groups revealed a higher rate of halitosis improvement in the SIBO-negative group (90.35% vs. 29.63%, P < 0.001), accompanied by significantly lower DMS levels (17.15 ± 5.81 ppb vs. 23.63 ± 9.99 ppb, P = 0.006). Therefore, we conclude that a four-week LFD intervention appears effective for refractory SIBO-associated halitosis, with great adherence and no risk of malnutrition. Its mechanism likely involves SIBO alleviation, thereby reducing intestinal production and breath excretion of volatile malodorous compounds, particularly DMS.