[Background] Neurospora crassa LY03 was the main fermentation strain isolated from traditional “Red fungus tofu” in Wuping. [Objective] The genomic information of Neurospora crassa LY03 strain was studied to reveal the fermentation characteristics of traditional “Red fungus tofu” in Wuping. [Methods] Morphological observation, ITS identification, resequencing and frame diagram sequencing were used to identify the isolated LY03 strains and analyzed the genome information. [Results] The main fermentation strain LY03 isolated from traditional “Red fungus tofu” in Wuping was identified as Neurospora crassa, and preserved in the China General Microbiological Culture Collection Center with preservation number CGMCC 3.1923. The total number of reads in LY03 strain compared to the reference genome was 95.85%, and the site of sequencing corresponding depth accounted for 76.13% of the whole genome. There was no variation in the intronic region of each variant type, and the main variation existed in the exon region of the genome, and the specific number of variation was as follows: The total number of SNP site variants was 203 128, InDel mutations was 26 859, copies increased and decreased by CNV was 1 039, variation in SV comments was 777. The genome sequence length of LY03 strain was 30 538 737 bp, (G+C)mol% was 52.24%, encoding 5 550 genes, accounting for 24.3% of the coding genes, which was involved in the metabolic pathway transformation of amino acid metabolism, carbohydrate metabolism, energy production and conversion and other substances. [Conclusion] The identification and genome information analysis of the main fermentation strains of traditional “Red fungus tofu” in Wuping are helpful to reveal the fermentation characteristics of the products and the essence of the genetic information of the fermentation strains, and to provide a theoretical basis for the improvement of the fermentation performance and the popularization of the products in the future.