The metabolites of gut microbiome are important host-health regulating factors and can be interrupted when the host is exposed to environmental pollutant via ingestion route. Arsenic contaminated drinking water is one of the most serious environmental health problems worldwide. Therefore, the arsenic-induced alterations of gut microbiome and metabolome, especially the persistence and reversibility of the alterations after the long-term arsenic exposure will be interesting to know. In this study, we investigated the relationship between gut microbiota and metabolites in male rats both after the 30-days arsenic treatment and 30-days recovery duration. The composition and diversity of gut microbiota were affected significantly by the treatment, but they presented partial improvement in recovery duration. Moreover, arsenic exposure induced the significant changes of 73 metabolites, which involved in the metabolism of glycerophospholipid, linoleic acid, as well as the biosynthesis of phenylalanine, tyrosine and tryptophan. Although it had a persistent effect, the restoration of glycerophospholipid metabolism was observed in the 30-days recovery. Integration analysis further correlated the arsenic impacting microbes with some important differential metabolites. Lactobacillus associated with the decreases of phosphatidylethanolamine(34:1), 16alpha-hydroxydehydroepiandrosterone 3-sulfate, seryltryptophan and alanyltyrosine in recovery duration. Lactobacillus strains have potential to work as protective agents against arsenic toxicity by restoring perturbed glycerophospholipid metabolism. In summary, arsenic significantly disrupted gut microbiome and metabolome, but the disruptions are reversible to some extent after a 30-days recovery.