Systematical screening of the metabolic profile of marine fungus Aspergillus sp. EGF 15-0-3 using OSMAC-GNPS molecular networking cascade followed by target isolation of the environmental-induced products resulted the identification of eight unprecedented indole diketopiperazine-based hybrids (1−8) featuring three distinct chemical backbones. The structures of the obtained compounds were established by combination of extensive spectroscopic analyses, X-ray crystallography, and ECD calculations. All these environmental-induced metabolites were demonstrated to be unusual tyrosyl-DNA phosphodiesterase 2 inhibitors. Compound 3, as the most outstanding example, showed selective synergistic antitumor effect when combined with the chemotherapeutic drugs.