Pomegranate (Punica granatum L.) has a long cultivation history in China, and is well-loved for its unique flavor, health benefits, and beautiful symbol. However, handling redundant genetic information from a large number of germplasms is inefficient for breeding program of pomegranate, so it is necessary to construct a core set with minimal germplasm sampling and maximal genetic diversity. In this study, the genetic diversity and population structure of 266 collected pomegranate germplasms were analyzed using 40 SSR molecular markers with high polymorphism, and an integrated core collection was developed based on the genetic information. A total of 193 fragments were amplified in the 266 germplasms, ranging from 2 to 18 per marker, with an average allelic richness of 4.825. The polymorphic information content (PIC) value for each marker ranged from 0.225 to 0.744. The germplasms collected from Central China showed the highest genetic diversity (H_o = 0.433, H_e = 0.531, and I = 0.912), which might be related to the strong inclusiveness for germplasms and frequent gene exchange in this area. Population structure analysis showed that these germplasms were appointed into four subpopulations. Based on the SSR data, three core sets with 56, 50, and 53 germplasms were developed by Power Core (PC), Core Finder (CF), and Core Hunter (CH) programs, respectively. Because both PC and CF follow the M-strategy and CH follows the genetic distance sampling strategy, an integrated core collection with 87 germplasms combining germplasms in the core sets generated by PC and CH was further developed to maximize the genetic distances and genetic diversity parameters. This integrated core collection showed a high genetic diversity level (N_a = 4.825, N_e = 2.431, H_o = 0.350, H_e = 0.549, and I = 0.981), which were not significantly different from those of the initial collection, demonstrating sufficient representativeness for the initial collection. The development of the core collection with 87 germplasms is valuable to support the breeding program of pomegranates.