Unsaturated loess slopes in the Three-River Source Region of Qinghai are prone to landslide hazards under rainfall infiltration. To investigate the influence of rainfall on slope stability in this region and the effectiveness of ecological slope protection, this study first determined the basic physical properties, shear strength under controlled matric suction (50–200 kPa), and soil-water characteristic curves of undisturbed samples through laboratory tests. A transient seepage–stress coupled finite element model (COMSOL) was then constructed to simulate slope responses under varying rainfall intensities, durations, and slope heights. The results show that when the matric suction increases from 50 kPa to 200 kPa, the cohesion increases by 153% and the internal friction angle increases by 65%. Rainfall infiltration increases water content and consequently reduces matric suction, causing the factor of safety (Fs) to decay nonlinearly. The most pronounced decline in Fs occurs under high-intensity (120 mm/d) and prolonged rainfall: for a 30 m slope, Fs drops below the engineering threshold of 1.25 after 1 day and falls below 1.0 after 3 days. Ecological protection using tall fescue roots (0.5 m depth) delays the advancement of the wetting front, yielding an Fs 16%–22% higher than that of a bare slope under identical rainfall, while also flattening the Fs degradation curve. These outcomes provide a quantitative basis for early warning and nature-based stabilization of loess slopes in high-altitude ecologically sensitive zones.