To screen the new wheat germplasm resistant to crown rot in Huang huai wheat area and establish the new identified method for the resistance which can distinguish the other disease in the basal straw of wheat, the resistance to crown rot of one hundred and eight varieties coming from Huang huai wheat area was evaluated by seedling survey method in the house and the DNA contents of Fusarium graminearum in the basal straw of forty-five wheat varieties were detected simultaneously by Real-time PCR so as to analyze the relationship between the DNA content of Fusarium graminearum and the resistance to crown rot of wheat. Twenty-two varieties with moderate resistance to crown rot were screened out, but no more resistant or immune varieties were found. The correlation analysis showed that, between the Fusarium graminearum DNA content in the basal straw of wheat and the average disease grade, there was significant correlation with the correlation coefficient 0.73, indicating that the Fusarium graminearum DNA content in the basal straw of wheat could be used as the important reference to determine the resistance to crown rot of wheat. The new wheat gerplasm and the Real-time PCR method used for the resistance evaluation will be helpful to breeding of wheat cultivar resistant to crown rot in Huang huai wheat area.