Agricultural production in the saline–alkaline soils of the Yellow River Delta faces persistent challenges in waste recycling and soil improvement. We developed a three-stage circular agriculture model integrating “crop straw–edible mushrooms–vegetables,” enabling simultaneous waste utilization and soil remediation within one year (two mushroom and two vegetable cycles annually). Crop straw was first used to cultivate Pleurotus eryngii, achieving 80% biological efficiency and reducing substrate costs by ~36.3%. The spent mushroom substrate (SMS) was then reused for Ganoderma lucidum and vegetable cultivation, maximizing the resource efficiency. SMS application significantly improved soil properties: organic matter increased 11-fold (from 14.8 to 162.78 g/kg) and pH decreased from 8.34 to ~6.75. The available phosphorus and potassium contents increased several-fold compared to untreated soil. Metagenomic analysis showed the enrichment of beneficial decomposer bacteria (Hyphomicrobiales, Burkholderiales, and Streptomyces) and functional genes involved in glyoxylate metabolism, nitrogen cycling, and lignocellulose degradation. These changes shifted the microbial community from a stress-tolerant to a nutrient-cycling profile. The vegetable yield and quality improved markedly: cabbage and cauliflower yields increased by 34–38%, and the tomato lycopene content rose by 179%. Economically, the system generated 1,695,000–1,962,881.4 CNY per hectare annually and reduced fertilizer costs by ~450,000 CNY per hectare. This mushroom–vegetable rotation addresses ecological bottlenecks in saline–alkaline lands through lignin-driven carbon release, organic acid-mediated pH reduction, and actinomycete-dominated decomposition, offering a sustainable agricultural strategy for coastal regions.