Lilium growth is severely impeded by continuous cropping, and crop rotation is essential to reducing the detrimental effects of monocultures. Soil (0–20 cm) was collected in three Lilium cropping patterns in Longshan County, Hunan Province, including continuous Lilium cropping (Lilium), corn upland rotation with Lilium (Corn), and paddy rotation with Lilium (Rice). Using Illumina high-throughput sequencing technology, the fungal ribosomal DNA internal-transcribed spacer 1 (ITS1) was examined to evaluate the features of soil fungi communities among three cropping patterns. Crop rotation has an impact on soil properties and the microbial community. Rice soil has a significantly higher pH than Lilium and corn soil, while corn and rice soil have a greater total nitrogen and total phosphorus content than Lilium soil. Rotation cropping clearly shifted the fungi community diversity based on the results of principal coordinate analysis (PCoA) and nonmetric multidimensional scaling (NMDS). Ascomycota was the most prevalent phylum, with the highest levels in Lilium soil. Genetic analysis revealed that paddy rotation led to a clear reduction in or non-detection of eight potentially pathogenic fungal genera and a noticeable accumulation of eight beneficial fungal genera compared to Lilium continuous cropping. Fungi communities and their abundant taxa were correlated with soil pH and nutrients. Altogether, we propose that rice rotation, with its ability to mitigate soil acidification, reducing pathogenic and accumulating beneficial communities, may be an effective strategy for alleviating the continuous cropping barrier.