This work was conducted to evaluate the total concentration and speciation of heavy metals (Cd, Pb and Cr) in vermicompost product (EFCD) by Eisenia fetida (EF) with cow dung (FCD). Meanwhile, the bacterial community and diversity of the three were compared by high-throughput sequencing. Results showed that heavy metal concentrations were declined significantly in EFCD. Sequential extraction indicated that the exchangeable fraction of Cd and Pb decreased markedly and the residual fractions increased in EFCD. Though the exchangeable fraction of Cr increased, the total concentration reduced greatly. Furthermore, the speciation of Cd, Pb and Cr bioaccumulated in EF were different. Besides, the bacterial diversity was highest in EFCD, and twelve genera with species having heavy metal resistance/tolerance were found from the genus of different abundance of the three. Vermicomposting effectively reduced the total concentration and toxicity for heavy metals, and the bacterial composition and diversity were changed greatly during vermicomposting.