Fructooligosaccharides (FOS) are widely used as bioactive ingredient in functional foods. In this study, we presented an efficient method to produce the FOS using a mutant strain of Aspergillus oryzae S719. This mutant strain hold an overexpressing β-fructofuranosidase (FTase) with high-level FOS synthetic activity and it was resistant to high osmotic pressure. At a sucrose concentration of 900 g/L, Aspergillus oryzae S719 produced 586.0 ± 4.7 g/L of FOS in a 50 L bioreactor during a 20 h transformation process, whose productivity was 2-fold higher compared to an initial sucrose concentration of 500 g/L. Scanning electron microscopy (SEM) revealed that the mycelia of Aspergillus oryzae S719 was loose and spherical and had a large number of vacuoles compared to the original strain Aspergillus oryzae ZT65. These morphological characteristics might have contributed to the improved FTase activity. In summary, this study demonstrated an efficient strategy for FOS production on an industrial scale.