Halophytes colonize stressed environments of high salinity. Endophytic symbionts improve growth performance and thus adaptability of host plants in stressed environments. Nevertheless, studies focused on the distribution and assembly patterns of fungal endophyte assemblages of halophytes in high salinity environments are limited. We selected 27 common non-mangrove halophytes across 4 geographic sites along the eastern coastline of China for our investigation on endophyte assemblages. We found a significant amount of basidiomycetous fungi in the endophyte assemblage. The endophyte community compositions were significantly affected by plant species and geographic locations. Some halophyte hosts showed significant preference for endophytic fungi in host preference analysis. The network structures of host-microbe bipartite graphs at each site had low connection and were highly nested, modular and specialized. Current results also indicated significant correlation and congruency between host phylogeny and compositions of endophyte local communities and meta-community. Our research showed that host is the dominant factor shaping the fungal endophytic communities in aerial tissues of halophytes in high salinity environments, and the host influence on endophytic community relates to plant phylogeny.