Maize ear rot is a worldwide serious fungal disease, and at present has become one of the main problems in maize growing areas. However, the measure against this disease remains difficult. In this study, a RIL population comprising 233 lines and a natural population comprising 452 backbone inbred lines were used for evaluating ear rot resistance. The cobs were inoculated with Fusarium verticillioides to observe their kernel resistance and cob resistance; while the kernels were inoculated with F. verticillioides to observe their cob resistance and kernel resistance. By comparing the kernel resistance observed by inoculating cob and kernel resistance observed by inoculating kernel, it was found that the kernel resistance observed by inoculating cobs of 114 lines in RIL population and 230 inbred lines in associated population was not consistent with their kernel resistance observed by inoculating kernel. By comparing cob resistance observed by inoculating kernel with cob resistance observed by inoculating cob, it was found that the cob resistance observed by inoculating kernel of 138 families in RIL population and 247 inbred lines in associated population was not consistent with their cob resistance observed by inoculating cob. Collectively, the interaction between kernel resistance and cob resistance may involve a new disease resistance mechanism, which deepened the understanding of the resistance mechanism of maize ear rot from a new perspective.