Corm rot is the most important disease of saffron, for which fungi from several genus such asFusariumspp.Penicilliumspp. andBotrytisspp., have been previously reported to be the pathogens. In this research, we used a combination of amplicon sequencing and traditional isolation methods to identify the causal agents, main infection source. The diversity of microbial communities in diseased saffron corms and soil decreased significantly compared with healthy corms and soil. The contents ofPenicilliumandBotrytisin healthy and diseased corms were similarly high, indicating that them were not directly related to the occurrence of corm rot. But the relative abundance ofFusarium,CadophoraandFusicollawere significantly higher in the diseased corms than healthy ones. The abundance ofFusariumincreased, while the abundance ofOidiodendron,Paraphaeosphaeriaand the endophytic beneficial bacteriaPseudomonasdecreased, which may relate to the occurrence of the disease. The co-occurrence network diagram showed that the correlation between fungal and bacterial communities was mainly positive. Plant pathogens were relatively abundant in the diseased soil, according to functional gene prediction. At the same time, we also collected 100 diseased corms from the fields in Jiande, where is known as the “hometown of saffron.” All isolated pathogenic strains were identified asFusarium oxysporumthrough morphological observation and phylogenetic tree analysis of ITS,Tef-1αandβ-tubulin. To better clarify the biological characteristics ofF.oxysporum, we cultured the isolates at different temperatures and pH values. The optimum temperature for mycelial growth and sporulation was 25°C, pH 6，carbon sources sorbitol and nitrogen sources, peptone. In short, our results suggests thatF. oxysporumwas the pathogen causing corm rot in Jiande and corms other than soils are the main primary infection source. These new understanding of saffron corm rot will provide the theoretical basis for its better and efficiently management.