Abstract: Ecological restoration is often required to reduce land degradation in mining areas. Among them, limestone quarry soils have restricted crop establishment due to severe compaction, high alkalinity, nutrient deficiencies, and low water-holding capacity. Active microalgal crusts can be expected to offer a biological intervention for soil remediation via extracellular polymeric substances (EPS) and immobilizing nutrients. However, it is still unclear about their concentration-dependent effects on the "algae-soil-crop" continuum in alkaline reclaimed soils. This study aims to evaluate the promotion effects of active microalgae on soil microenvironments and wheat growth. The optimal inoculation threshold was then determined to identify the key driving factors. A pot experiment was conducted using reclaimed topsoil from a limestone mine. Three inoculation concentrations of Microcoleus vaginatus (using chlorophyll-a density: 5, 10, and 20 μg/cm², denoted as A1, A2, and A3) were established, along with uninoculated (CK) and culture medium (BG11) controls. Wheat developmental quality was tracked at the tillering and overwintering stages. Furthermore, 13 plant traits were monitored—covering biomass, morphology, root architecture, and physiological stress markers—and 15 soil physicochemical properties. A Random Forest (RF) model was used to quantify the feature importance of environmental drivers, according to the wheat quality index (WQI) as the dependent variable. Active microalgae exhibited a "low-promotion and high-inhibition" concentration-dependent threshold. A2 treatment (10 μg/cm²) emerged as the optimal threshold, with an increase in seed germination rate by 18.50 percentage points compared with the CK. Meanwhile, A2 treatment optimized root architecture during subsequent growth, significantly expanding total root length and surface area. Additionally, the subterranean network also drove macro-phenotypic improvements. Tillering-stage wheat dry weight and plant height increased by 89.42% and 34.83%, respectively. Mechanistically, microalgal proliferation yielded massive EPS accumulation, which cemented soil fragments, reduced bulk density for water retention, and aeration. An enriched matrix provided a well-buffered pore network that facilitated nutrient mass flow toward root surfaces. A positive feedback loop was established as the "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). A2 treatment mitigated lipid peroxidation, where malondialdehyde (MDA) content dropped by 33.88%. Cascade activation of antioxidant defenses was attributed to mark as increased catalase (CAT) and peroxidase (POD) activities. Notably, A2 treatment maintained significantly higher enzyme activities than the CK during the overwintering stage, thus preserving robust reactive oxygen species (ROS) scavenging capacity under low-temperature stress. Enzymatic superiority effectively prevented cell membrane destruction during the harsh winter period. Furthermore, the soluble sugars and proteins were synchronously accumulated to adjust cellular osmotic behavior, providing for physiological toughness against soil alkalinity and winter cold. Soil organic matter (OM, 11.52%), available phosphorus (AP, 10.72%), and soil water content (SWC, 10.35%) were identified as the primary limiting factors, indicating the moisture and nutrient requirements. The algal crust development quality index (ADQI, 8.31%) also ranked highly, indicating the cross-interface synergistic regulation by microalgae. On the plant end, the feature weight hierarchy (Growth > Root > Physiology) revealed an adaptive survival prioritizing structural morphogenesis and photosynthetic area preservation under extreme stress. Thus, leaf number and biomass represented reliable diagnostic targets to monitor plant health. In conclusion, inoculating active Microcoleus vaginatus at 10 μg/cm² can serve as an effective, sustainable biotechnology for mine soil reclamation, thus bridging micro-ecological engineering and macro-agricultural rehabilitation. This finding can offer a practical reference to optimize microbial application dosages in large-scale ecological engineering in arid or alkaline mining wastelands.