Characterization of the salt-tolerance function in microbial communities is important for understanding the soil and sediment biodiversity distribution near saltern affected by the environmental factors. Here, we combined high-throughput sequencing of 16S rDNA and ITS to investigate the distribution and salt-tolerance function of microbial communities in coastal soils and sediments present near Yinggehai saltern field of Hainan Island, China. The microbial communities in the soil and sediments of the land zone (YGHLS), the intertidal zone (YGHIS), and inshore zone (YGHWS) were compared. PCoA of weighted and unweighted UniFrac distances showed the difference in soil microbial communities across the samples. ANOSIM analysis revealed that the three samples were separated from each other. Halomonas , Halobacillus and Wallemia presented in the samples and accounted for 0.0335 ± 0.0586%, 0.0241 ± 0.0304% and 0.0308 ± 0.0445% of the total microbial community. Relative abundance of Na + :H + antiporter, Trk system potassium uptake protein and Kdp operon response regulator in the samples exceed 0.02%, 0.09% and 0.06% respectively. It revealed that the halotolerant bacteria of Yinggehai coastal soil and sediment mainly take the Trk system for salt-tolerance function.