Background: To investigate the diagnostic value of arterial spin labeling (ASL) and intravoxel incoherent motion (IVIM) imaging in distinguishing nasopharyngeal carcinoma (NPC) in T1 stage from healthy controls (HC). Methods: Forty-five newly diagnosed NPC patients in the T1 stage and thirty-one healthy volunteers who underwent MR examinations for both 3D pseudo-continuous ASL (pCASL) and IVIM were enrolled in this study. The Mann-Whitney test was used to compare the mean values of blood flow (BF) derived from pCASL and IVIM derived parameters, including apparent diffusion coefficient (ADC), pure molecular diffusion (D), pseudo-diffusion coefficient (D*) and perfusion fraction (f) between NPC tumor and benign nasopharyngeal mucosa of HC. Receiver Operating Characteristic (ROC) was performed to determine diagnostic cutoff and efficiency. The correlation coefficients among parameters were investigated using Spearman's test. Results: The NPC in the T1 stage showed higher mean BF, lower ADC, D, and f compared to benign nasopharyngeal mucosa (P < 0.001) with the area under curve of ROC of 0.742-0.996 (highest by BF). BF cutoff was set at > 36 mL/100 g/min; the corresponding sensitivity, specificity, and accuracy in differentiating NPC stage T1 from benign nasopharyngeal mucosa were 95.56% (43/45), 100% (31/31) and 97.37% (74/76), respectively. BF demonstrated moderate negative correlation with D* on HC (ρ [Spearman correlation coefficients] = − 0.426, P = 0.017). Conclusions: ASL and IVIM could reflect the difference in perfusion and diffusion between tumor and benign nasopharyngeal mucosa, indicating a potential for accessing early diagnosis of NPC. Notably, BF, with a specificity of 100%, demonstrated better performance compared to IVIM in distinguishing malignant lesions from healthy tissue.