Lung cancer is the leading cause of cancer-related mortality worldwide. Phospholipase D6 (PLD6) found to be highly expressed in lung cancer and plays a key role in activating Wnt/β-catenin signaling by enhancing mitochondrial metabolism. PLD6 acts as an oncogenic switch by promoting mitochondria-mediated signaling, thereby regulating Wnt signaling in cancer cells. The enzyme activity of PLD6 depends on dimerization. This study aimed to develop anticancer drugs targeting PLD6 dimerization through structure-activity relationship (SAR) analysis. Several compounds showing over 90% inhibition activity were identified, including a quinoxaline-based structure which was selected as the hit compound. Then, novel quinoxaline derivatives were designed and synthesized as lead compounds to improve effectiveness and selectivity. This research established a synthetic scheme for developing lead compounds targeting PLD6 dimerization. The quinoxaline-based inhibitors represent a promising new class of anticancer agents with potential therapeutic applications in lung cancer treatment through specific targeting of PLD6-mediated oncogenic signaling pathways.