<p>Yellowhorn (<i>Xanthoceras sorbifolium</i> Bunge) is a woody oil species endemic to China. Its oil is predominantly composed of unsaturated fatty acids (UFAs, 85–93%), including the functional component nervonic acid. The kernels were approved as a new food raw material in 2023, highlighting their nutritional and economic value. However, research on differences in kernel nutritional composition and metabolite components among its main cultivars remains insufficient, and no analysis of quality variation among widely cultivated high-yield cultivars from major production regions in China has been conducted. This study compared the main nutrient compositions in kernels from seven yellowhorn cultivars (lines) using gas chromatography (GC), gas chromatography-mass spectrometry (GC–MS), and high-performance liquid chromatography (HPLC), and conducted the first investigation of widely targeted metabolites in kernels from three representative types using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The results showed significant variation in nutrient content across the analyzed samples—LG08 exhibited the highest oil and total fatty acid content, and the highest comprehensive quality among the tested accessions, representing a promising genetic material for high-quality variety breeding. A total of 782 metabolites were identified, with 164–324 showing significant differences. The differential metabolites were significantly enriched in pathways, including ABC transporters and biosynthesis of amino acids, indicating that differences in kernel nutrient accumulation among cultivars may be related to genetic variations in transmembrane transport and primary metabolic regulation. These results provide data supporting the further breeding, processing, and industrial utilization of yellowhorn kernels.</p>