Halophytes harbour unique rhizosphere microbial communities as a result of their unique habitat. The rhizosphere soil fungal diversity and community structures of four halophytes, including Kalidium foliatum, Lycium ruthenicum, Karelinia caspia and Phragmites australis, typically distributed in the arid land of Southern Xinjiang, were studied using the Illumina high-throughput sequencing technology. The study aims to reveal the alpha diversity, species composition, abundance and the differences of rhizosphere soil fungi among the four halophytes, explore their correlation with environmental factors to provide the basis for further investigation of the relationship between rhizosphere soil microbes and salt tolerance of halophytes. The results showed that the physicochemical characteristics of the rhizosphere soil of the four halophytes were different. The soil pH was all over 8.0, and the electronic conductivity (EC) value from high to low was Phragmites australis, Kalidium foliatum, Karelinia caspia, Lycium ruthenicum. The soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (AN) and available phosphorus (AP) contents in the rhizosphere soil of Lycium ruthenicum were the highest, while the SOM, TN, TP, TK and AN values were the lowest in Phragmites australis, but the SWC and EC value were the highest. The numbers of operational taxonomic units (OTUs) unique to Kalidium foliatum, Lycium ruthenicum, Karelinia caspia, and Phragmites australis were 51, 19, 11, and 53 respectively, as well as their common OTUs number was 153. The fungi community richness (abundance-based coverage estimator, ACE and Chao 1 index) from high to low was Kalidium foliatum, Phragmites australis, Lycium ruthenicum, and Karelinia caspia. The fungal community was different in composition and abundance in the rhizosphere of the four halophytes. A total of 8 phyla, 21 classes, 44 orders, 89 families, and 124 genera fungi were detected in their rhizosphere soil samples. The relative abundance and distribution of fungi varied at phylum level, and the dominant groups were Ascomycota, Basidiomycota, and Chytridiomycota. There were 11, 9, 8, and 6 genera with relative abundance greater than 1% in the rhizosphere soil of Kalidium foliatum, Lycium ruthenicum, Karelinia caspia, and Phragmites australis, respectively, with 4 common dominant genera including Fusarium, Acremoniuma, Aspergillus and Penicillium. The number of non-dominant fungi was large but the relative abundance varied with plant species. Then each plant had its particular or mutual fungal genera with different abundance, some of which were affected greatly by soil physicochemical properties. According to canonical correlation analysis (CCA), we found that the major influence factors that caused the change of soil fungal community structures of the four halophytes were oil available potassium, available phosphorus, pH and electrical conductivity. This study revealed that the rhizosphere soil fungi communities of the four halophytes were similar, but the abundance of dominant bacteria was significantly different, with plant species specificity. The rhizosphere fungi community was correlated with the soil environmental factors.