Molybdenum (Mo) is one of the essential nutrient element for the plant growth,but excess Mo will cause physiological toxicity to plant. With the increase of mining area,many events of Mo pollution have been reported in the world. Meanwhile,many studies have found that some plants show strong tolerance to excessive Mo,but there are few studies on the Mo tolerance mechanisms. Therefore,we analyzed the changes of Mo content in subcellular components and leaf metabolites of wheat under excess Mo supply,and to further explore the physiological mechanism. The Mo content in cell wall,soluble part,organelle,protoplast/chloroplast of root subcellular components was 219,38,25 and 62 times higher than that in shoot respectively; The accumulation proportion of Mo in soluble fraction of root and shoot was 71.85% and 88.54%. Under excess Mo,the contents of malic acid and fumaric acid in wheat leaves were increased by 2.08 and 2.07 times,and the contents of βalanine,Lserine,Lthreonine and Lglutamine were increased by 2.78,1.89,1.67 and 1.91 times,respectively. These results indicate that root system can prevent and control the transportation of excess Mo to shoot,and vacuole can be the main storage site of excess Mo，and organic acids and amino acids produced may chelate with Mo in vacuole to reduce its biological toxicity. This study provided theoretical basic for the mechanism of plant tolerance to excess Mo stress,and supplied the technical support for plant remediation of soil Mo pollution.