The purpose of this study is to determine whether multiparametric non-contrast MR imaging including diffusion-weighted imaging (DWI), arterial spin labeling (ASL), and amide proton transfer (APT) weighted imaging can help differentiate malignant from benign salivary gland lesions. The study population consisted of 42 patients, with 31 benign and 11 malignant salivary gland lesions. All patients were evaluated using DWI, three-dimensional pseudo-continuous ASL, and APT-weighted imaging on 3 T MR imaging before treatment. Apparent diffusion coefficient (ADC), tumor blood flow (TBF), and APT-related signal intensity (APTSI) values within the lesion were compared between the malignant and benign lesions by Mann-Whitney U test. For each parameter, optimal cutoff values were chosen using a threshold criterion that maximized the Youden index for predicting malignant lesions. The performance of ADC, TBF, APTSI, individually and combined, was evaluated in terms of diagnostic ability for malignant lesions. Diagnostic performance was compared by McNemar test. APTSI was significantly higher in malignant lesions (2.18 ± 0.89%) than in benign lesions (1.57 ± 1.09%, p = 0.047). There was no significant difference in ADC or TBF between benign and malignant lesions (p = 0.155 and 0.498, respectively). The accuracy of ADC, TBF, and APTSI for diagnosing malignant lesions was 47.6%, 50.0%, and 66.7%, respectively; whereas the accuracy of the three parameters combined was 85.7%, which was significantly higher than that of each parameter alone (p = 0.001, 0.001, and 0.008, respectively). Therefore, the combination of ADC, TBF, and APTSI can help differentiate malignant from benign salivary gland lesions.