Abstract: A transition method from discrete molecular dynamics (MD) simulation to continuum elastic finite element analysis (FEA) is proposed. Firstly, the moving position and displacement of crystal material atoms is obtained by MD calculation, and then the finite element deformation model under the assumption of continuous medium is constructed according to the characteristics of crystal structure. Further, the strain and stress fields are obtained combined with the constitutive relationship of material mechanical behavior. In order to test the effectiveness of the MD-FEA method, this method is applied to analyze the tensile deformation of Al-Ni soft-hard composite nano cylinder and the nano indentation of substrate Al with spherical diamond indenter. The stress and the strain fields of the above two problems are obtained by MD-FEA method, and the calculated results are compared with the atomic strain calculated by discrete deformation gradient and the atomic potential stress in traditional MD method. The difference between the stress and strain field calculated by MD-FEA method and the traditional MD atomic strain and potential stress is discussed in detail, and the effectiveness of MD-FEA method and its advantages over traditional MD method are discussed. The result shows that the MD-FEA method and the traditional MD method are consistent when the stress and strain change softly in the volume, and in the area where stress and strain change rapidly and in the surface/interface area, the MD-FEA method can calculate the result more precise. Meanwhile, the MD-FEA method avoid the selection of the cutoff radius and weighting functions, which is necessary in traditional MD method and can lead to human error in some circumstances. When the strain is large, there are obvious difference between the small strain calculated by MD-FEA method and the Green strain calculated by traditional MD method. Thus the MD-FEA method is more suitable for the situation that the stress and strain is small.