Oral microbial dysbiosis is the primary etiologic factor for halitosis and may be the critical preventive target for halitosis. This study included randomized controlled trials (RCTs) assessing the effects of Lactobacillus paracasei ET-22 live and heat-killed bacteria on halitosis and the related oral microbiome. 68 halitosis subjects were divided into placebo, ET-22 live (ET-22.L) and ET-22 heat-killed (ET-22.HK) groups. Subjects took different lozenges three times a day for 4 weeks and underwent saliva collection and assessment of breath volatile sulfur compound (VSC) levels at the beginning and end of the intervention. Salivary volatile organic compounds were measured using HS-SPME-GC/MS, and the microbiome profile was determined by 16S rRNA gene amplicon sequencing. A positive decrease in breath volatile sulfur compound (VSC) levels was observed in the means of both ET-22.L and ET-22.HK groups after 4 weeks of intervention, being more marked in the ET-22.L group (p = 0.0148). Moreover, ET-22.L and ET-22.HK intervention remarkably changed the composition of total salivary volatile organic compounds (VOCs) and aroma-active VOCs. Key undesirable VOCs, such as indole, pyridine, nonanoic acid, benzothiazole, and valeric acid, were significantly reduced. Meanwhile, ET-22.L or ET-22.HK also altered the taxonomic composition of the salivary microbiome. The halitosis pathogens Rothia and Streptococcus were significantly reduced in the ET-22.HK group and the pathogenic Solobacterium and Peptostreptococcus were significantly inhibited in the ET-22.L group. Collectively, our study suggests that both ET-22.L and ET-22.HK can significantly inhibit the production of undesirable odor compounds in subjects with halitosis, which may be related to the changes of the oral microbiome.