China’s loess deposits exhibit high vulnerability to deformation under precipitation and snowmelt, posing significant risks to infrastructure. This study utilized enzyme-induced carbonate precipitation (EICP) to enhance the mechanical properties of Yili loess. Comparative analyses of untreated and EICP-treated samples were conducted using unconfined compression strength (UCS) tests, unconsolidated–undrained (UU) triaxial shear tests, and scanning electron microscopy (SEM). Results demonstrated that urease activity increased markedly between 25–65 °C, while calcium carbonate production peaked at 55 °C before declining. EICP treatment elevated UCS by 52% relative to untreated soil and altered the failure mechanisms: untreated specimens failed through penetrating shear cracks, whereas treated specimens exhibited compressive failure with vertical fissures. Triaxial tests confirmed enhanced properties in EICP-stabilized loess, showing 8.3–10.7% higher failure strength and 15.7% greater cohesion (increasing from 31.3 kPa to 36.2 kPa), while the internal friction angle remained largely unchanged. Microstructural analysis revealed that EICP generated continuous cementitious layers and crystal bridges of vaterite, transforming particle contacts from point-to-point to surface-to-surface interfaces. Simultaneously, crystal precipitation reduced pore sizes and increased tortuosity. These micro-scale modifications improved interparticle friction constraints and stress transfer efficiency, thereby enhancing the macroscopic mechanical performance. The findings validate EICP’s efficacy for stabilizing collapsible loess deposits and provide insights for geohazard mitigation in similar engineering contexts.