Purpose Comprehensive understanding glioma metabolic characters is of great help for patient management. We aimed to compare amide proton transfer imaging (APTw) and magnetization transfer imaging (MT) in predicting glioma malignancy and reflecting tumor proliferation. Methods Thirty low-grade gliomas (LGGs) and 39 high-grade gliomas (HGGs) were prospectively included, of which 58 samples Ki-67 levels were quantified. Anatomical MRI, APTw, and MT were scanned, and magnetization transfer ratio (MTR) and asymmetric magnetic transfer ratio at 3.5 ppm (MTRasym(3.5ppm)) were calculated. ROIs were semi-automatically drawn with ImageJ, from which histogram features, including 5th, 25th, 50th, mean, 70th, 90th, and 95th percentiles were extracted. The independentttest was used to test differences in LGGs and HGGs, and correlations between histogram features and tumor grades, Ki-67 were revealed by Spearman's rank or Pearson's correlation analysis. Results The maximum correlation coefficient (R) values of APTw were 0.526 (p< 0.001) with tumor grades and 0.397 (p< 0.001) with Ki-67 at 90th percentiles, while only 5th and 25th percentiles of MT significantly correlated with tumor grades. Moreover, APTw features were significantly different in LGGs and HGGs, except 5th percentile. The most significantly different feature was 95th percentile, providing the excellent AUC of 0.808. However, the best feature in MTR was 5th percentiles with AUC of 0.703. Combing 5th and 95th of APTw achieved highest AUC Of 0.837. Conclusions Both APTw and MT provide quantitative information for tumor metabolite imaging. However, APTw supplys more specific information in reflecting glioma biological behaviors than MT, and well differentiates glioma malignancy.