China is a large country in the production of edible fungi. In order to further enhance the industrial innovation ability, increasing the basic research on edible fungi is the key breakthrough point. In recent years, with the rapid development of biotechnology, omics-drive research on edible fungi has shifted from phenotype description to systematic mechanism analysis. The application of single omics technology has achieved extensive progress in the genetic basis, gene regulation, protein dynamics, metabolic pathways, and phenotypic analysis of edible fungi. However, the problems of one-sided and fragmented data of single omics can be addressed only through integrated analysis of multi-omics. Therefore, multi-omics technology has gradually become the core driver for the paradigm shift in research on genetic breeding of edible fungi. Although the current research still faces challenges such as data quality, functional verification, computing resources, and integration complexity, future researches should focus on innovations in underlying technologies, AI-driven approaches, cross-scale integration, the construction of resource platforms, etc. Continued promotion of deep integration and innovative application of multi-omics will facilitate high-quality development of the industry of edible fungi, thereby meeting the needs of food security and public health.