High-temperature stress adversely affects the yield and quality of red clover (Trifolium pratense). However, the molecular mechanisms underlying red clover’s heat tolerance remain incompletely understood, which limits targeted genetic improvement. This study employed a multi-omics approach to compare a heat-tolerant cultivar (“HL”) and a heat-sensitive cultivar (“Tp615”). Under high-temperature stress, “HL” exhibited superior physiological adaptation, showing 1.8 times higher chlorophyll retention compared to “Tp615.” Transcriptome analysis identified 3104 core differentially expressed genes, including 175 transcription factors, with qRT-PCR validation confirming expression patterns consistent with the transcriptomic data. Broad-targeted metabolomics revealed 1242 differentially accumulated metabolites. Multi-omics integration highlighted the crucial role of the phenylpropanoid biosynthesis pathway in enhancing red clover’s heat tolerance. This study deciphers the mechanisms underlying red clover’s heat resistance and offers valuable genetic resources and a theoretical foundation for breeding stress-tolerant forage crops.