The Loess Plateau is a typical dry farming area in China. Film mulching—a widely used practice in this region—can be further deplete the poor soil organic matter levels. Straw incorporation can alleviate the adverse environmental impact of film mulching and increase crop yield. However, few studies have investigated the effects of continuous straw incorporation with film mulching on the soil fungal community in the Loess Plateau of China. This study compared the effects of straw incorporation (S) and without straw incorporation (NS) under ridge–furrow plastic film mulch on fungal community structure, fungal network structure, soil quality, and maize yield in a four-year experiment. At the end of the experiment, the soil under S had greater soil fungal richness than the soil under NS. The fungal community had greater stability and complexity and more competition and cooperation between fungi under S than NS. The stochastic process played a stronger role in constructing the fungal community under NS than S. Continuous straw incorporation changed the key dominant species from Agaricomycetes, Dothideomycetes, and Leotiomycetes under NS to Ascomycetes under S. The pathogenic fungal population significantly increased by 166% under S. Changes in the soil fungal community under S were mainly affected by increasing soil moisture, total phosphorus, and total nitrogen. Continuous straw incorporation improved soil quality with increased soil urease and catalase activities and soil organic carbon and available phosphorus contents. In four years, S significantly increased the maize yield by 4–15% compared with NS treatment. In sum, continuous straw incorporation changed the fungal community composition, improved the relationships between fungal communities and soil quality, contributing to the increased maize yield under S. The results of this study could promote the sustainable development of agriculture, which has great significance for the wider application of straw incorporation in China and elsewhere.