OBJECTIVES: This study aimed to compare the diagnostic performance of magnetocardiography (MCG) and coronary computed tomography angiography (CCTA) in detecting coronary artery stenosis in relation to coronary calcification. METHODS: A total of 587 patients who underwent invasive coronary angiography (ICA) with both CCTA and MCG between September 1, 2022, and August 31, 2023, were included. The patients were divided into three subgroups based on their coronary artery calcium score (CACS), namely less than 100, 100-400, and 400 and above, as determined by the Agatston score. The diagnostic sensitivity, specificity, accuracy, and the area under the receiver operating characteristic curve (ROC) of MCG, CCTA, and the combined diagnostic model (CCTA + MCG) were compared across all CACS subgroups. RESULTS: According to ICA, 481 out of 587 patients (81.94%) had ischemia. The area under the ROC curve (AUC) of MCG for detecting ischemia was 0.80, with a sensitivity of 74.64% and specificity of 84.91% for all patients. In the different CACS subgroups, the diagnostic specificity of CCTA notably decreased (78.57% vs 24.13% vs 17.46%), while that of MCG remained stable (92.86% vs 86.21% vs 82.54%). The diagnostic accuracy of MCG and the combined diagnostic model was better than that of CCTA when CACS was ≥ 400 (77.22% vs 67.22% vs 58.89%). The AUC values of MCG, CCTA, and the combined model in the CACS ≥ 400 subgroups were 0.78, 0.49, and 0.71, respectively. CONCLUSIONS: The diagnostic performance of MCG is less affected by CACS than that of CCTA. MCG and the combined model demonstrate better performance than CCTA alone in detecting coronary artery stenosis, particularly in cases with CACS ≥ 400. KEY POINTS: Question How does the diagnostic performance of MCG compare with coronary computed tomographic angiography (CCTA) at different levels of calcification scores (CACS)? Findings MCG demonstrated better performance than CCTA in detecting coronary artery stenosis, particularly in patients with high CACS. Clinical relevance MCG or the MCG and CCTA combined model can be used to improve the noninvasive imaging diagnostic performance for detecting coronary artery stenosis and reduce unnecessary ICA, especially for patients with high calcification scores.