Objective To explore the relationship between the Ebola virus genome variations and its epidemiological characteristics by analyzing the 102 whole genome sequences of Ebola viruses in 2014 outbreak. Methods Whole genome sequences of Ebola viruses (EBOVs) were obtained from the NCBI database, and the variations in genome sequences were analyzed by Mummer3.0. The evolutionary analysis was carried out through MEGA5; and the 3D modeling of the protein was performed using CPHmodels and PyMOL software. Results It was found that there were 606 single nucleotide variants (SNVs) in the genome of 2014 EBOVs, of which 49 nonsynonymous SNVs were unique. The amino acids of NP-182, GP-82 and L-1951, which were highly conserved not only among all the Zaire EBOVs before 2014, but also among different EBOV species, were altered in 2014 EBOVs. Conclusion The unique mutation of 2014 EBOVs resulting in alterations of NP, GP and L protein, especially the alteration of aa82 of GP (Ala→Val), might weaken the stability of α-helix where the amino acid is located, which might be associated with the weakened lethality and enhanced transmission of the virus. Further studies are needed to confirm whether genomic variations in 2014 EBOVs is responsible for change of the epidemiological characteristics.