The strain tensors are commonly defined by the local deformation of continuum. Unlike displacement, strain is not a physical quantity that can be measured directly, and it is calculated from a definition that relies on the gradient of the continuous displacement field. At the microscale, it is difficult to define the local deformation according to the position of each atom which is obtained from the adjacent discrete time interval, so there is no universally accepted definition of strain tensors of atomic scale so far, and none of the molecular dynamics software can be used to calculate the atomic strain until now. In order to define the atomic scale strain, a method for calculating the "deformation" both in the atomic scale and the continuum scale is proposed. In the definition, the discrete deformation gradient is proposed to describe the "deformation" in the atomic scale and the influence weight function of neighborhood atom is introduced. Then the weighted least squares error optimization model is established to seek the optimal coefficients of the weight function and the optimal local deformation gradient of each atom. After that, the advanced multilayer complex genetic algorithm can be used to calculate the atomic strain. Finally, take NiTi alloy as an example, the molecular dynamics evolution model of deformation and failure of NiTi alloy was established. Then the atomic scale strain nephogram at each time was calculated, and the microdefects such as twins were observed by strain nephogram. Compared with the micro-observation experiment of crack tip of NiTi alloy for three-point bending, the rationality of the atomic scale strain definition method established in this study and its application significance in identifying the evolution of microdefects are verified.