Abstract: Varies of microstructure and nutritional quality of wheat seeds after application of nano fertilizer 399 are studied in this paper.The exterior topography and profiles features of wheat seeds are observed and compared between those applied with the nano fertilizer 399 and those not applied with the nano fertilizer 399 by Scanning Electron Microscope (SEM).From the observation of the wheat seeds with SEM,it is found that the 399 has the functions of promoting all of the growth of the epidermal cells,the aleurone layer and the albumen.In addition,the wheat applied with and those not applied with the 399 are detected in four aspects respectively,that is,the quality percentages of protein,fat,coarse fibres and heavy metal Pb.The results indicate that the wheat applied with the nano fertilizer 399 has significantly increased contents of both protein and fat.The contents of coarse fibres and Pb has no positive correlation with the application of the 399 nano fertilizer.