Eucommia ulmoides is a quaternary glacial ancient plant. As a traditional Chinese medicine plant，Eucommia tree is among the few woody plants which contains hardy rubber around the world. Except for Hevea brasiliensis，Eucommia tree is one of the most potential natural rubber resources and a strategically important resource for Chinese rubber reserve. To comprehensively analyze the genomic structure，locate the key function genes，study the origin and evolution and reveal the genetic blueprint in Eucommia ulmoides，the refined genome map of Eucommia ulmoides was completed based on shortgun and combining the second and third sequencing to overcome the difficulty in assembling complicated genome sequences. The results showed that the genome of E. ulmoides has a large genome size about 1.02 G. Its heterozygosity and repeatitive sequence are 0.9%～1.1% and 66%，respectively. The problem of short Scaffold in sequence length of Scaffold N50 over 932 kb was solved. After annotation，we found more than 26 thousand genes and over 3377 non-coding RNAs. Among these genes，one part of key genes associated with rubber synthesis were found that was result in the upstream synthesis pathway was determined；the genes and members related to the major medicinal components being found including phenylpropanoids，flavonoid，alpha linolenic acid；the genes or transcription factors being found related to the environmental stress including heat-resisting，anti-cooling，anti-drought，water stress，salt and alkali stress，anti-insect，and anti-disease，etc.；which will exhibit the molecular mechanism in wide adaptability. And the genes being found related to the sex will be an efficient approach for exhibiting the sex identification mode. With the refined genome map of Eucommia ulmoides was completed，the results will provide a basis for application research，including the efficient synthesis pathway of Eucommia rubber，the accumulation mechanism of medicinal component，the ability enhancement of the stress resistance，and the uncovering of the sex identification mode and revealment the origin and evolution，etc. The series of research fruits of genome sequencing can not only break through breeding problems at higher rubber content and medicinal component，but also is a milestone for new Eucommia rubber resources cultivation.