Background: Wen Dan Decoction (WDD) is primarily utilized as an "expectorant" in clinical practice. The combination of WDD and Lian Qiao (LQWDD) exhibits synergistic effects on phlegm resolution, qi regulation, and detoxification. In preliminary clinical practice, we observed that LQWDD effectively alleviates the severity of gastric precancerous lesions. Nevertheless, the underlying mechanism remains elusive. Purpose: This study was designed to explore the efficacy and potential mechanisms of LQWDD against gastric carcinogenesis. Methods: Retrospective analyses of patients with gastric precancerous lesions and an N-methyl-N9-nitro-N-nitrosoguanidine (MNNG)-induced rat gastric cancer model were conducted to evaluate the efficacy of LQWDD against gastric carcinogenesis. Proteomic analyses were employed to investigate the underlying mechanisms of LQWDD. Moreover, energy metabolites were quantified using metabolomics. Network pharmacology and highperformance liquid chromatography-mass spectrometry were integrated to elucidate the potential active components of LQWDD. Additionally, seahorse analysis and RNA sequencing were used to explore the effects and underlying mechanisms of compound quercetin on oxidative phosphorylation. Results: LQWDD effectively impeded gastric carcinogenesis in an MNNG-induced rat gastric cancer model and patients. Proteomic analyses revealed that LQWDD protected the integrity of the oxidative phosphorylation pathway during gastric carcinogenesis, which was significantly suppressed in human gastric intraepithelial neoplasia and MNNG-induced gastric carcinoma. Moreover, LQWDD administration significantly reversed MNNG-induced reductions in the expression of mitochondrial complex I-related proteins (ALDH3A1 and NDUFS4), as well as in ATP, NAD+, and metabolite levels, indicating its protective role against oxidative phosphorylation dysfunction through the modulation of mitochondrial complex I-associated proteins. Furthermore, quercetin and kaempferol were identified as potential active components of LQWDD. These components suppressed the growth of gastric cancer cells and patient-derived organoids while simultaneously increasing intracellular ATP and NAD+ levels. Notably, quercetin exerted its preferential regulatory role in mitochondrial oxidative respiration by activating the AMPK signaling pathway. Conclusions: Our study provides the first systematic evidence that mitochondrial OXPHOS dysfunction plays a pivotal role in gastric carcinogenesis. LQWDD and its potential active ingredient quercetin inhibit gastric carcinogenesis by mitigating oxidative phosphorylation impairment, highlighting on a promising therapeutic prescription for treating with gastric precancerous lesions.