Background: This study aimed to investigate the connection between malnutrition evaluated by the Controlling Nutritional Status (CONUT) score and the risk of contrast-associated acute kidney injury (CA-AKI) in elderly patients who underwent percutaneous coronary intervention (PCI). Methods: A total of 1308 patients aged over 75 years undergoing PCI was included. Based on the CONUT score, patients were assigned to normal (0–1), mild malnutrition (2–4), moderate-severe malnutrition group (≥ 5). The primary outcome was CA-AKI (an absolute increase in ≥ 0.3 mg/dL or ≥ 50% relative serum creatinine increase 48 h after contrast medium exposure). Results: Overall, the incidence of CA-AKI in normal, mild, moderate-severe malnutrition group was 10.8%, 11.0%, and 27.2%, respectively (p < 0.01). Compared with moderate-severe malnutrition group, the normal group and the mild malnutrition group showed significant lower risk of CA-AKI in models adjusting for risk factors for CA-AKI and variables in univariate analysis (odds ratio [OR] = 0.48, 95% confidence interval [CI]: 0.26–0.89, p = 0.02; OR = 0.46, 95%CI: 0.26–0.82, p = 0.009, respectively). Furthermore, the relationship were consistent across the subgroups classified by risk factors for CA-AKI except anemia. The risk of CA-AKI related with CONUT score was stronger in patients with anemia. (overall interaction p by CONUT score = 0.012). Conclusion: Moderate-severe malnutrition is associated with higher risk of CA-AKI in elderly patients undergoing PCI.