Effects of Stropharia rugosoannulata–Tomato Rotation Coupled with Spent Mushroom Substrate Incorporation on Soil Fertility, Yield and Fruit Quality of Tomato

Continuous monocropping of tomato causes soil degradation, secondary salinization, and yield decline. Mushroom–vegetable rotation coupled with spent mushroom substrate (SMS) incorporation offers a recycling strategy to mitigate these obstacles. Here, a five-stage progressive field experiment (2023–2025, Yantai, Shandong, China) was conducted to screen the optimal local configuration of Stropharia rugosoannulata–tomato rotation and reveal its soil improvement mechanisms. The combination of variety Nieyang and an apple woodchip-based substrate achieved the highest mushroom yield, with the substrate formula (F = 11.64, p = 0.0006) dominating productivity. Deep incorporation of SMS into the 0–20 cm plow layer (M treatment) avoided the seedling stress and mortality caused by surface mulching and increased the marketable yield of the large-fruited tomato R35 by 28.0% (79,560 kg·ha−1, p < 0.05) without altering fruit soluble solids (p = 0.611). Two consecutive rotation years increased soil organic carbon by 17.6% (from 3.29 to 3.87 g·kg−1) and total nitrogen by 243% (from 0.79 to 2.71 g·kg−1) and raised soil desalination efficiency from 33.5% to 56.2%, while soil EC and pH remained within the optimal range for tomato growth. Cross-regional verification showed universal regulation of soil pH and EC but background-dependent nutrient accumulation. The system improves soil fertility through mycelium-mediated biological desalination, progressive SMS-derived carbon pool accumulation, and complementary acid–base homeostasis, generating a net annual economic benefit of approximately 255,000 CNY·ha−1 (≈38,060 USD·ha−1). This recyclable rotation pattern is suitable for popularization in Jiaodong facility-grown tomato production.