Genetic diversity is crucial to genetic research and crop breeding, and core collections are important resources for capturing this diversity. Recently, the core germplasm of tea plants was constructed mainly based on phenotypic data or molecular markers; however, the effective construction of core germplasm resources for plant breeding programs requires consideration of multiple aspects. In this study, we collected 320 tea germplasm resources and analyzed their single-nucleotide polymorphisms (SNPs) and metabolite data. Abundant genetic diversity in tea plants was inferred from the mean values of observed heterozygosity (Ho=0.340), expected heterozygosity (He=0.327), minor allele frequency (MAF=0.229), and polymorphic information content (PIC=0.268), based on the data from 2,118,060 high-quality SNP markers. A mean genetic diversity index (H’) value of 1.902 suggested significant metabolic variation. The 320 tea samples were categorized into six groups based on phylogenetic analysis, reflecting the influence of geographical origins on genetic diversity. Based on the genetic and metabolic data, a preliminary core collection of 106 accessions was developed to effectively represent most of the original panel’s molecular, metabolic, population, and regional diversity. Genome-wide association studies of the core panel successfully replicated the marker-trait associations found in the original panel. This study contributes to the conservation and management of tea plant germplasm.