In this paper, three ectomycorrhizal fungi were inoculated to Pinus thunbergii seedlings. The ectomycorrhizal morphologies, as well as root hair growth and mantle, hartig net distribution were observed. The morphology of different ectomycorrhizas was various. The dominant forms of ectomycorrhizas developed by Rhizopogen luteous(R1) and Pisolithus tinctorius(Pt2) were coralloid branching, dichotomous branching, and multilevel dichotomous branching. The dominant forms of ectomycorrhizas developed by Boletus edulis(Be) were dichotomous branching and club-shaped ectomycorrhiza with a enlarged apex. The morphologies of ectomycorrhizas seemed not obviously correlated with the seedlings growth. Root hairs were observed in ectomycorrhizal short root. It showed some significant correlation with the seedlings growth. The percentage of ectomycorrhizal short roots with root hairs was higher in R1 and Pt2 than that in Be treatment. At the same time, many Hartig net hyphae were observed in the growth region of root hairs in the former, but many other fungi were observed in Be and the control treatment. This study was helpful to understand the root hairs growth and their function in the ectomycorrhizas. It was also useful to further explore the reciprocity and coevolution between the host plant and mycorrhizal fungi.