In this paper, Illumina MiSeq high-throughput sequencing was used to study the compositions and diversities of rhizosphere microbial community structures in three growth stages (pre-growth, fast-growing, and late-growth) of kiwifruit seedlings, and CANOCO and R language software were used for the analyses of RDA and correlation to disclose the relationship between soil fungal community and environmental factors. The results showed that significant differences existed in soil properties in different growth periods of kiwifruit seedlings. With continuous growth of roots, soil pH, available nitrogen and phosphorus increased first and then decreased, while available potassium gradually decreased. A total of 1 776 fungal OTUs were obtained by high-throughput sequencing, which belonged to 157 genera, 10 families, 22 classes and 151 families. Variation analysis showed that Shannon indexes were significantly different between different growth periods. Sequence analysis found that Ascomycota (72.69%), Mortierellomycota (18.80%), Rozellomycota (6.68%), Basidiomycota (4.28%) and Glomeromycota (1.45%) were the dominant phyla in different growth stages (the abundance greater than 1% is regarded as the dominant phylum), and Ascomycota increased first and then decreased while Mortierella, Rozelomycota and Basidiomycota decreased first and then increased. The relative abundance of Glomeromycota increased with the growth of roots. RDA analysis showed that soil available phosphorus and pH were significantly positively correlated with Ascomycota, available potassium negatively correlated with Ascomycota, and organic carbon significantly negatively correlated with Chytridiomycota. In conclusion, different rhizosphere soil fungal community structures were different in different growth periods of kiwifruit seedlings, the population of rhizosphere fungi was the most abundant in the fast-growing period and the least in the later growth period. Ascomycota, Mortierella, Rhodobacter and Basidiomycota were always the dominant rhizobacteria in the growth period of kiwifruit seedlings, rhizosphere fungi community composition and soil nutrients were different in different growth periods of kiwifruit seedlings, and soil available phosphorus and potassium were the important factors affecting the composition of ascomycetes community.