This study aimed to investigate the relationship between microvascular status in the non-ischemic myocardium and the diagnostic performance of stress dynamic CT perfusion imaging (CTP) in detecting hemodynamically significant stenosis. This study included 157 patients who underwent coronary computed tomography angiography (CTA), CTP, and invasive coronary angiography (ICA), including fractional flow reserve (FFR). Hemodynamically significant stenosis was defined by FFR and ICA. A relative myocardial blood flow (MBF) for each myocardial segment was normalized to the highest MBF (remote MBF) among 16 segments. The receiver operating characteristic curve analysis for detecting hemodynamically significant stenosis at the vessel level indicated that patients with lower, intermediate, and higher remote MBF had areas under the curve (AUC) of 0.66, 0.70, and 0.80, respectively, for absolute MBF and AUCs of 0.63, 0.70, and 0.83, respectively, for relative MBF. The optimal cut-off values for absolute MBF were proportional to the levels of remote MBFs, while the ones for relative MBF were more consistent across lower to higher remote MBFs. For the patients with high remote MBF, the relative MBF demonstrated a sensitivity of 69%, specificity of 88%, and accuracy of 85% in detecting hemodynamically significant stenosis. The microvascular status in the non-ischemic myocardium influenced the diagnostic performance of dynamic CTP and threshold values of absolute MBFs, suggesting the potential preference for relative MBF over absolute MBF in clinical settings. Dynamic CTP's quantification of MBF offers the benefit of indicating reliability in ischemia detection relative to microvascular status. Question The relationship between microvascular status and diagnostic performance of dynamic CTP imaging has not been fully investigated. Findings The diagnostic performance of dynamic CTP and threshold values of absolute MBF were impacted by microvascular status. Clinical relevance The differences in diagnostic accuracy of dynamic CTP related to varying remote MBF values necessitate a personalized evaluation of myocardial perfusion in dynamic CTP images.