In this study, the sediment cores were collected from two areas with or without vegetation covering in the intertidal zone of the Yellow River estuary, in which the characteristics and functional differences of bacterial community were analyzed based on real-time fluorescent quantitative PCR and high-throughput sequencing. The mainly environmental influencing factors were also explored. Results showed that the bacterial abundance from the vegetation area was higher than that from the vegetation-free area. The richness and diversity of bacterial community increased with the depth in the vegetation area, while they were the highest in the sample of middle layer (14-16 cm) in the vegetation-free area. The shared dominant phyla in both areas were Proteobacteria, Chloroflexi, Actinobacteria and Acidobacteria. The dominant genera were Bacillus, Ochrobactrum, Amycolatopsis, Sphingomonas and so on. The results of correlation analysis showed that salinity and nitrite concentration were the main influencing factors of the richness and diversity of bacterial community. The functional prediction analysis showed that the processes of bacterial membrane transport, amino acid metabolism and carbohydrate metabolism in the vegetation area were more active, while the processes of bacterial DNA replication, repairing and energy metabolism in the vegetation-free area were more active.