Abstract: Ecological restoration in degraded mining areas is a critical challenge. Limestone quarry soils typically suffer from severe compaction, high alkalinity, nutrient deficiencies, and poor water-holding capacity, restricting crop establishment. Active microalgal crusts offer a biological intervention for soil remediation by secreting extracellular polymeric substances (EPS) and immobilizing nutrients. However, their concentration-dependent regulatory mechanisms and effects on the "algae-soil-crop" continuum in alkaline reclaimed soils remain unclear. This study evaluated the promotion effects of active microalgae on soil microenvironments and wheat growth, determined the optimal inoculation threshold, and identified the core driving factors. A pot experiment used reclaimed topsoil from a limestone mine. Three inoculation concentrations of Microcoleus vaginatus (based on chlorophyll-a density: 5, 10, and 20 μg/cm², denoted as A1, A2, and A3) were established, alongside uninoculated (CK) and culture medium (BG11) controls. Wheat developmental quality was tracked at the tillering and overwintering stages. We monitored 13 plant traits—covering biomass, morphology, root architecture, and physiological stress markers—and 15 soil physicochemical properties. A Random Forest (RF) model, using the comprehensive wheat quality index (WQI) as the dependent variable, quantified the feature importance of environmental drivers. Active microalgae exhibited a "low-promotion and high-inhibition" concentration-dependent threshold effect. The A2 treatment (10 μg/cm²) emerged as the optimal threshold, increasing the seed germination rate by 30.38% compared to CK. During subsequent growth, A2 optimized root architecture, significantly expanding total root length and surface area. This enhanced subterranean network drove macro-phenotypic improvements, increasing tillering-stage wheat dry weight and plant height by 89.42% and 34.83%, respectively. Mechanistically, microalgal proliferation yielded massive EPS accumulation, which cemented soil fragments, reduced bulk density, and improved water-retention and aeration. The enriched matrix provided a well-buffered pore network that facilitated nutrient mass flow toward root surfaces.This established a positive feedback loop of "crust development–soil optimization–robust root establishment–leaf area expansion–photosynthetic intensification" at the algae-soil-wheat interface. Physiologically, the algal crust bolstered the plants' systemic acquired resistance (SAR). The A2 treatment mitigated lipid peroxidation, dropping malondialdehyde (MDA) content by 33.88%. This was driven by the cascade activation of antioxidant defenses, marked by increased catalase (CAT) and peroxidase (POD) activities. Notably, A2 maintained significantly higher enzyme activities than CK during the overwintering stage, preserving robust reactive oxygen species (ROS) scavenging capacity under low-temperature stress. This persistent enzymatic superiority effectively prevented cell membrane destruction during the harsh winter period. Furthermore, the synchronous accumulation of soluble sugars and proteins enhanced cellular osmotic adjustment, providing physiological toughness against soil alkalinity and winter cold. The RF model identified soil organic matter (OM, 11.52%), available phosphorus (AP, 10.72%), and soil water content (SWC, 10.35%) as the primary limiting factors, emphasizing the need for moisture and nutrient management. The algal crust development quality index (ADQI, 8.31%) also ranked highly, verifying the cross-interface synergistic regulation by microalgae. On the plant end, the feature weight hierarchy (Growth > Root > Physiology) revealed an adaptive survival strategy prioritizing structural morphogenesis and photosynthetic area preservation under extreme stress. Thus, leaf number and biomass represent reliable diagnostic targets for monitoring plant health. In conclusion, inoculating active Microcoleus vaginatus at 10 μg/cm² provides an effective, sustainable biotechnology for mine soil reclamation, bridging micro-ecological engineering and macro-agricultural rehabilitation. This study offers a practical reference for optimizing microbial application dosages in large-scale ecological engineering projects within arid or alkaline mining wastelands.