Postharvest quality deterioration of Korla fragrant pear (Pyrus sinkiangensis Yu) severely constrains its market value, yet the regulatory role of pre–harvest soil management in shaping postharvest performance remains poorly understood. This study investigated how green manure species modulate postharvest quality trajectories and their underlying soil–fruit linkages. Three pre–harvest treatments were imposed: control (CK), sweet clover (CM), and alfalfa (MX). Fruits were harvested and stored at 4 °C, with sampling at 1, 5, 10, 15, and 20 d. A critical quality transition was identified at 15 d, characterized by the concurrent peaking of soluble sugars, organic acids, vitamin C, and anthocyanins alongside an optimal sugar–acid ratio. Beyond this inflection point, CM and MX diverged markedly: CM enhanced soluble sugar accumulation, anthocyanin retention, and ester volatile production—most notably hexyl acetate, which increased over 14.4–fold—thereby generating a pronounced fruity aroma bouquet. Conversely, MX sustained higher amino acid and vitamin C levels and conferred superior late–storage stability, evidenced by a threefold lower coefficient of variation in sugar–acid ratio relative to CK. partial least squares structural equation modeling (PLS–SEM) revealed soil fertility as the principal driver of fruit quality, but the fidelity of soil–to–fruit transmission was species–dependent. MX achieved near–complete explanatory power (R²= 0.971), whereas CM exhibited attenuated transmission fidelity (R²= 0.777), with network analysis further indicating that CM inverted the polarity of key soil–fruit correlations. These findings demonstrate that green manure identity governs postharvest quality through divergent soil–fruit coupling pathways: alfalfa optimizes nutrient transmission efficiency and stabilizes nutritional quality, whereas sweet clover promotes sugar–aroma accumulation at the cost of reduced soil–fruit conversion fidelity. Species–specific green manure selection thus offers a viable strategy for targeted modulation of postharvest traits in Korla fragrant pear.