Sequencing technologies make it possible to explore uncultured microorganisms since they can be used to obtain the species composition information of research objects and further study the information at the functional gene level. The commonly used sequencing methods include amplicon sequencing and metagenomic sequencing. Postharvest fruits and vegetables harbor a large number of microorganisms. But most current studies on microorganisms on agricultural products focus only on a few pathogens or a single antagonist, so that little is known about the diversity and composition of microbial communities on agricultural products and the factors that influence their structures. Therefore, this review summarizes recent studies evaluating the microbial community structure on agricultural products by sequencing, describes the definition of microbiome and related terms and the major sequencing methods, and discusses recent progress in the application of microbiom sequencing technologies in postharvest fruits and vegetables. Furthermore, it discusses the factors limiting the application of microbiom technology in the field of postharvest fruits and vegetables and puts forward some possible future research directions. Hopefully, this review will provide a theoretical basis for future studies on the microbiome of fruits and vegetables after harvest.