Background: While both cystatin C and left ventricular ejection fraction (LVEF) revealed established prognostic efficacy in coronary artery disease (CAD), the relationship between cystatin C/left ventricular ejection fraction ratio (CLR) and adverse clinical outcomes among patients with CAD following percutaneous coronary intervention (PCI) remains obscure, to date. Therefore, we sought to assess the predictive efficacy of CLR among CAD patients who underwent PCI in current study. Methods: A total of 14,733 participants, including 8622 patients with acute coronary syndrome (ACS) and 6111 patients with stable coronary artery disease (SCAD), were enrolled from a prospective cohort of 15,250 CAD patients who underwent PCI and were admitted to the First Affiliated Hospital of Xinjiang Medical University from 2016 to 2021. The primary outcome of this study was mortality, including all-cause mortality (ACM) and cardiac mortality (CM). The secondary outcomes were major adverse cardiovascular events (MACEs), major adverse cardiac and cerebrovascular events (MACCEs) and nonfatal myocardial infarction (NFMI). For CLR, the optimal cut-off value was determined by utilizing receiver operating characteristic curve analysis (ROC). Subsequently, patients were assigned into two groups: a high-CLR group (CLR \ge0.019, n = 3877) and a low-CLR group (CLR 0.019, n = 10,856), based on optimal cut-off value of 0.019. Lastly, the incidence of outcomes between the two groups was compared. Results: The high-CLR group had a higher incidence of ACM (8.8% vs. 0.9%), CM (6.7% vs. 0.6%), MACEs (12.7% vs. 5.9%), MACCEs (13.3% vs. 6.7%), and NFMIs (3.3% vs. 0.9%). After adjusting for confounders, multivariate Cox regression analyses revealed that patients with high-CLR had an 8.163-fold increased risk of ACM (HR = 10.643, 95% CI: 5.525~20.501, p 0.001), a 10.643-fold increased risk of CM (HR = 10.643, 95% CI: 5.525~20.501, p 0.001), a 2.352-fold increased risk of MACE (HR = 2.352, 95% CI: 1.754~3.154, p 0.001), a 2.137-fold increased risk of MACCEs (HR = 2.137, 95% CI: 1.611~2.834, p 0.001), and a 1.580-fold increased risk of NFMI (HR = 1.580, 95% CI: 1.273~1.960, p 0.001) compared to patients with low-CLR. Conclusions: The current study indicated that a high CLR is a novel and powerful predictor of adverse long-term outcomes in CAD patients who underwent PCI, and that, it is a better predictor for patients wtih SCAD and ACS. Clinical Trial Registration: NCT05174143, http://Clinicaltrials.gov.