Head smut of corn is caused by the fungus Sphacelotheca reiliana and occurs in northeast China and in regions of a similar climate. Yield losses due to the disease are variable and directly depend on the severity of the disease. The objective of this study was to produce a coating technology to protect corn from head smut and to avoid environmental pollution. Based on its excellent properties of high efficiency, nonpollution and nontoxicity, a novel seed coating agent was prepared with modified chitosan as the main material and trace elements and fertilizer as the auxiliary material. Compared with the conventional toxic seed coating agent, the novel seed coating agent protected the seeds and provided excellent control of head smut and increased yield by 11.6 to 14.6%, while the cost of seed coating agent decreased by 32.4%. Our findings indicate that the application of chitosan in seed coating technology had a remarkable effect on the resistance to head smut of corn and yield enhancement.