Biotic elicitor is an important biotechnology strategy to promote metabolite production in adventitious root culture. In this study, Panax ginseng adventitious roots (PGARs) were co-cultured with sterilized mycelium powders (SMPAN), immobilized mycelium (IMAN), and immobilized spores of Aspergillus niger (ISAN) respectively for the enhancement of ginsenosides accumulation. In this co-cultivation system, ISAN was selected as the best inducer. The maximum ginsenosides content (26.43 ± 0.49 mg/g) were obtained in the ISAN spore concentration of 102 spores/mL, the volume ratio of 4%, and co-culture time of 24 h, which was 3.09 times higher than non-treated control (8.55 ± 0.78 mg/g). Besides, the lactic acid secreted by A. niger was identified as the main component inducing ginsenosides accumulation. Moreover, this study revealed that lactic acid could trigger the instantaneous accumulation of signaling molecules and enhance the expression of transcription factors and defense genes in PGARs, thus resulting in the up-regulated expression of functional genes involved in ginsenosides biosynthetic pathway. Therefore, co-culture of ISAN and PGARs is a very promising method to increase ginsenosides production. It provides a new way to promote the accumulation of secondary metabolites in plants.