Idiopathic halitosis is an unusual condition of unclear causes, which has never been thoroughly investigated. We aimed to explore the role of small intestinal bacterial overgrowth (SIBO) in the pathogenesis of idiopathic halitosis, and to evaluate the therapeutic efficacy of a probiotic preparation on this condition. This retrospective observational study included 162 idiopathic halitosis patients and 198 healthy controls (HCs). Halitosis was diagnosed using the organoleptic test (OLT), and idiopathic halitosis was diagnosed by excluding known causes. SIBO was identified through the hydrogen/methane lactulose breath test (LBT), and accordingly, patients were identified as SIBO-positive or SIBO-negative. Idiopathic halitosis patients were treated with the probiotic preparation Bifidobacterium triple viable capsule for two months, followed by re-evaluation of halitosis and SIBO. This study found that all cases of idiopathic halitosis were extra-oral. The SIBO positivity rate in idiopathic halitosis patients was significantly higher than that in HCs (74.69% [121/162] vs. 3.03% [6/198], P < 0.001), with an odds ratio (OR) of 94.44 (95% CI: 39.99-211.35). After treatment, 80.17% (97/121) of the SIBO-positive patients became SIBO-negative. Moreover, 87.60% (106/121) of the SIBO-positive patients experienced improved halitosis, a rate significantly higher than that observed in SIBO-negative patients (2.75%, 3/41) (P < 0.001). In addition, 98.97% (96/97) of the post-treatment SIBO-negative patients experienced improved halitosis, a rate significantly higher than that of post-treatment sustained SIBO-positive patients (41.67%, 10/24) (P < 0.001). Our findings suggest that idiopathic halitosis is an extra-oral condition which mostly originates from the small intestine. SIBO is one of its underlying causes. The probiotic preparation can effectively improve idiopathic halitosis, probably through its impact on SIBO.