Ground covers in orchards, including clover, play a crucial role in soil carbon sequestration. However, the molecular composition of soil organic matter (SOM) and its role in regulating carbon persistence following clover establishment remain unclear. Using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) technology, this study quantified the effects of different clover cover durations (0, 2, 9, and 19 years) in apple orchards on the molecular composition, diversity, and complexity of SOM. Additionally, the relationships between soil physicochemical factors and SOM composition, as well as the potential sources of different SOM functional groups, were investigated. As soil depth increased, the proportions of N-compounds, polysaccharides and phenols decreased, while the proportions of aliphatics and terpenoids increased. This was accompanied by a decline in SOM oxidation states with increasing soil depth. Increased clover cover duration promoted the overall accumulation of SOM, and the relative accumulation of N-compounds, polysaccharides and phenols in deeper soil layers. Water extractable organic carbon (WEOC) emerged as a key predictor of the observed variance in SOM molecular composition, while N-compounds were significantly correlated to SOM molecular complexity. Further, prolonged clover cover increased SOM molecular alpha-diversity, but simplified its interaction networks, potentially improving carbon persistence. These findings underscore the potential of perennial ground covers like clover to enhance soil organic carbon (SOC) accumulation by promoting molecular diversity and regulating SOM network architecture, offering a promising strategy for sustainable soil carbon management in arable systems.