In this study, a multiplex PCR-based SNP genotyping panel was developed using genotyping-by-sequencing (GBS) data, which includes 170 of core SNP markers. To analyze the genetic diversity of 202 pepper germplasms and identify associated loci for phenotypic traits, this study conducted genetic diversity and association analyses on 202 pepper germplasms using the SNP panel and 30 phenotypic traits. Research showed that a total of 170 core SNP markers distributed across 12 chromosomes, and the average Shannon's Information index, polymorphic information content (PIC) and Nei's gene diversity was 0.616, 0.334 and 0.428, respectively. This indicate high genetic diversity among the tested materials. Results from cluster analysis, population structure analysis, and principal coordinate analysis were consistent: all divided the tested materials into five groups, with each group showing a certain correlation with geographical origin and fruit characteristics. The coefficient of variation (CV) for 30 phenotypic traits ranged from 7.00% to 87.88%, with an average of 40.58%. Genetic diversity index (H′) varied from 0.03 to 2.07, with an average of 1.19. Among these traits, single fruit weight showed the highest CV (87.88%), while fruit length had the highest H′ (2.07). Corolla color exhibited the lowest values for both CV (7.00%) and H′ (0.03). Most of the 30 phenotypic traits showed significant or highly significant correlations. Furthermore, association analysis was performed between phenotypic traits and SNP markers. And the results showed that a total of 53 SNP-associated loci were detected by the two methods (GLM and MLM), which were significantly associated with 12 phenotypic traits. GLM and MLM can explain 4.83%–48.41% and 10.86%–19.19% of the phenotypic variance, respectively. And the marker 980-003 located on chromosome 4 has the highest phenotypic variance explained for corolla color. Four loci were simultaneously detected by both methods. The SNP genotyping panel developed in this study is a genotyping method with high throughput, good accuracy, and low cost, which can be applied to studies such as genetic structure analysis, molecular marker-assisted breeding, and variety identification of peppers. In addition, this study established a database of phenotypic traits and genotypes for 202 pepper germplasms, effectively establishing the corresponding relationship between phenotype and genotype. It provides theoretical guidance and material basis for the exploration of excellent pepper genes, germplasm innovation and the genetic improvement of varieties.