Fungal endophytes, as an untapped resource of glycoside hydrolase biocatalysts, need to be further developed. The primary active compound in the fruit of Momordica grosvenorii, mogroside V, can be converted into other various bioactive mogrosides by selective hydrolysis of glucose residues at C3 and C24 positions. In present study, 20 fungal strains were randomly selected from our endophytic fungal strain library to investigate their capability for transforming mogroside V. The results revealed that relatively high rate (30%) endophytic fungal strains exhibited the ability of transformation. Further analysis indicated that endophytic fungi could produce abundant mogrosides, and the pathways for biotransforming mogroside V showed diverse. Among the given fungal endophytes, Aspergillus sp. S125 could almost completely transform mogroside V into the end-products mogroside II A and aglycone only after 2 days of fermentation; Muyocopron sp. A5 produced rich intermediate products, including siamenoside Ⅰ, and the end-product mogroside II E. Furthermore, Aspergillus sp. S125 and Muyocopron sp. A5 were selected to optimize the fermentation conditions in order to evaluate the feasibility of large-scale conversion of mogroside V. After optimization, Aspergillus sp. S125 could convert 10 g/L of mogroside V into 4.5 g/L of mogroside II A and 3.6 g/L of aglycone after 3 days of fermentation, while Muyocopron sp. A5 could selectively produce 4.88 g/L of siamenoside Ⅰ from 7.5 g/L of mogroside V after 36 hours of fermentation. This study not only provides a class of highly effective biocatalytic candidates for transform mogrosides, but also strongly indicates that plant endophytic fungi can be used as a potential resource for biocatalysis of natural compounds.