Extensive mining of rare earth deposits has caused severe soil erosion, resulting in the degradation of plant–soil systems and the reduction in microbial diversity. Combined ecological remediation technology is the key method of vegetation reconstruction and ecological restoration in abandoned tailings. In this study, the effects of different cover crops–biochar–organic fertilizer and biochar–organic fertilizer treatments on soil fungal communities in rare earth tailings soil were analysed using high-throughput sequencing technology. Linear discriminant analysis effect size (LEfSe) was used to analyse saprophytic, mycorrhizal, and potential pathogenic fungi in soils after different combined remediations. Moreover, the effects of soil environmental factors on fungal community species’ composition were analysed by redundancy analysis (RDA) and variance partitioning analysis (VPA) after different combined remediations. LEfSe indicated a risk of citrus pathogenicity by Diaporthaceae indicator fungi after biochar–organic fertilizer combined treatment. RDA and VPA revealed that pH was the main environmental factor affecting the fungal community in the different combined remediation treatments. Additionally, the Paspalum wettsteinii cover crops–biochar–organic fertilizer and biochar–livestock manure treatments were more conducive to arbuscular mycorrhizal fungi recruitment. We also clarified the fungal community composition structure, soil environmental factors, and fungal community relationships in rare earth tailings soil after different combined remediation treatments.