We explored the ability of an Aspergillus niger α-glucosidase displayed on P. pastoris to act as a whole-cell biocatalyst (Pp-ANGL-GCW61) system to synthesize isomalto-oligosaccharides (IMOs). IMOs are a mixture that includes isomaltose (IG), panose (P), and isomaltotriose (IG). In this study, the IMOs were synthesized by a hydrolysis-transglycosylation reaction in an aqueous system of maltose. In a 2 mL reaction system, the IMOs were synthesized with a conversion rate of approximately 49% in 2 h when 30% maltose was utilized under optimal conditions by Pp-ANGL-GCW61. Additionally, the 0.5-L reaction system was conducted in a 2-L stirred reactor with a conversion rate of approximately 44% in 2 h. Moreover, the conversion rate was relatively stable after the whole-cell catalyst was reused three times. In conclusion, Pp-ANGL-GCW61 has a high reaction efficiency and operational stability, which makes it a powerful biocatalyst available for industrial scale synthesis.