Platycodon grandiflorum A. DC (Campanulaceae) is a traditional medicinal plant. Its root, Platycodi Radix, contains an abundant amount of saponin glycosides, platycodins, of which platycodin D is one of the major components. The chemical structures of platycodins can be modified by various types of chemical processing, but a modification mediated with microorganisms has been not reported yet. In this study, platycodin D was modified to several partially degraded platycodin glycosides after treatment with a crude enzyme extract from Aspergillus niger (A. niger). The modified platycodin D possessed a shorter sugar side-chain, and presented a remarkably reduced V79-4 cell (Chinese hamster lung fibroblasts) cytotoxicity and erythrocyte hemolytic toxicity, whereas the nitrite-scavenging activity was increased in the modified platycodin D. Sensory scores for pungency, bitterness and after-taste were improved as well in the modified platycodin D. Results suggest that A. niger mediated modification yielded a novel partially degraded platycodin glycoside which possesses increased bioactivities and improved sensory values, yet with reduced toxic profiles.