Natural rubber from Hevea brasiliensis serves as an irreplaceable industrial raw material. Whether rubber-yield potential is constrained by sucrose-sink sucrose partitioning remains incompletely understood. Here, we integrated transcriptomics and targeted sugar metabolomics across leaves, bark and latex from three H. brasiliensis clones with contrasting yields (designated H, M, and L). Transcriptomic profiling revealed tissue-specific functional differentiation: leaves were enriched in photosynthetic carbon fixation, bark in substance transport, and latex in defence and regeneration. The H clone did not show enhanced transcriptional enrichment of photosynthetic pathways relative to the L clone. Instead, it displayed a higher transcript abundance of invertase and sucrose synthase genes alongside elevated hexose levels, pointing to putative genotypic differences in sucrose hydrolysis and hexose turnover. Metabolomic profiling revealed greater sucrose accumulation in leaves of the L clone, accompanied by relatively low sucrose concentrations in latex. WGCNA analysis identified the MEpink module as strongly correlated with leaf sucrose content. This module is enriched in thiamine and cyanoamino acid metabolism and contains candidate transcription factors WRKY40, MYC2 and NAC002. Our results suggest that yield variation among these clones correlates with distinct sucrose distribution and utilization profiles. These multi-omics signatures provide a molecular resource to support high-yield rubber tree breeding.