The Luochuan area is an important area for apple production in China. With the renewal and transformation of aged apple orchards, the occurrence of apple replant disease (ARD) was inevitable and has seriously affected the sustainable development of apples. Therefore, we randomly selected 14 soil samples from aged apple orchards in the Luochuan area to study the structural changes in the soil fungal community. The results showed that there were significant differences in the diversity of fungal communities between different aged apple orchards. The harmful fungi Gibberella, Fusarium, and Cryptococcus existed in 14 aged apple orchards in the Luochuan area, but their abundances were different in different aged apple orchards. A FUN Guild analysis showed that fungi were mainly present in the aged apple orchards in Luochuan in the saprotroph and pathotroph nutrition modes. Pathogenic fungi were widely present, which increased the risk of disease and seriously affected the growth and development of fruit trees. To sum up, there was a strong correlation between the ages of orchards and the unbalanced microbial community structure. Therefore, pathogenic fungi could be prevented and controlled during the renewal and transformation of aged orchards to reduce the impact of ARD on the apple industry.