Developing novel copper-based complexes as potential chemotherapeutic agents is a great challenge in antitumor medicine. In this study, we aimed to reveal a benzimidazole-quinoline copper-based complex 1 induced antitumor activity in human gastric cancer. Complex 1 induced oxidative stress and increase the level of intracellular ROS expression. Further, complex 1 induced proliferation inhibition, mitochondrial dysfunction, G2/M phase arrest and apoptosis. In addition, transcriptome analysis revealed that cell migration, invasion, cycle and death behaviors were related to genetic changes intracellular. PPI network and molecular docking analysis discovered the potential interaction sites, which can be used as the discovery of chemotherapeutic agent or to improve treatment strategies.