As a key tropical economic tree species, the girth of the rubber tree (Hevea brasiliensis) not only reflects its growth rate and timber yield but also determines tapping schedules and non-productive periods. This trait critically influences both the species’ economic value and latex production potential. Despite recent advances in genetic analyses of girth driven by genomic technologies, the number of identified key genes remains insufficient to support molecular breeding programs. This study focuses on 138 samples of rubber tree natural accessions, integrating phenotypic data analysis, population genetic structure analysis, and genome-wide association analysis (GWAS) to identify genetic loci and candidate genes associated with girth. Population stratification divides the tested accessions into four genetic groups: Groups Ⅰ and Ⅳ exhibit high genetic purity, while Groups Ⅱ and Ⅲ display hybrid characteristics. GWAS based on a mixed linear model detects 7 and 23 SNPs significantly associated with girth at p = 4.4 × 10⁻⁸ and p = 2.22 × 10⁻⁷, respectively. The most significant SNP is located at position 44994744 on chromosome CM021229.1. Under the highly significant association threshold, 27 candidate genes were identified, 4 of which are directly related to girth. Gene Ontology (GO) annotation of these 27 candidate genes reveals their primary involvement in metabolic regulation, signal transduction, and cell component construction. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis shows they are primarily enriched in the “aminoacyl-tRNA biosynthesis” and “glycolysis/gluconeogenesis” pathways. These findings provide significant theoretical support for genetic enhancement and mechanistic analysis of rubber tree growth traits. They reveal novel SNP markers and genes that complement existing genetic resources, refining breeding strategies for elite genotype selection and ultimately contributing to enhanced rubber production.