The invention relates to an L-malic acid high-yield strain and application thereof. The strain is classified and named as Aspergillus niger L01, and has a deposit number of CCTCC NO: M 2019458. The Aspergillus niger L01 is a mutant strain with high yield of L-malic acid obtained by subjecting Aspergillus niger CICC NO: 40567, purchased from the China Center of Industrial Culture Collection (CICC),as a starting strain, to ARTP physical mutagenesis combined with natural screening. The mutant strain has a high yield of L-malic acid, can not only solve a problem of aflatoxin production in a fermentation process of Aspergillus flavus strains, but also directly use existing excess citric acid production device to promote the transformation and upgrading of the enterprise as technology for producing citric acid from Aspergillus niger is mature in the industry.