Abstract: This study compared the leaf length, corm weight, diameter, perimeter, nutrient accumulation, and the key medicinal component crocin between Chongming and Dutch corms. Additionally, Illumina MiSeq high-throughput sequencing technology was used to analyze microorganism difference of diseased corms of saffron from different provenances. The results showed that under the rice-saffron rotation system, Dutch corms exhibited remarkable advantages, including longer leaves and green periods, faster corm growth, and abundant accumulation of nutrients, particularly a significantly higher crocin content compared with Chongming corms. During storage, the incidence rates of rot disease in Chongming and Dutch corms were 6.67% and 6.00%, respectively, with the Dutch corms showing a slightly lower rate. Nevertheless, the microbial community composition of both types displayed a high degree of similarity. Further analysis revealed that the primary pathogenic factors of saffron corm rot were Penicillium and Fusarium genera, yet the potential combined infection of common aquatic bacteria such as Flavobacterium and Novosphingobium, as well as fungi like Cadophora luteo-olivacea, which frequently appears in rot diseases of other crops (grapes, kiwifruits), cannot be overlooked. This study preliminarily clarified the growth characteristics of saffron from different provenances and the microbial diversity and community structure in their diseased corms, providing a solid theoretical foundation and scientific basis for the introduction, evaluation, and efficient utilization of saffron crocus germplasm resources.