It has been shown that heterogeneity at the micro-structure level can effectively enhance the strength and ductility of materials. Here we demonstrate via density-functional theory calculations that high entropy alloys (HEAs) exhibit atomic level heterogeneity in bond length and stacking fault energy (SFE) which could lead to HEAs’ excellent hardenability and deformability. The bond length of HEA FeCoNiCrCu follows a Gaussian distribution, in contrast to the single-valued SFE and bond length in conventional crystalline counterparts. Its SFEs also fall into a wide span, which could introduce sequential and dispersed nucleation of different plastic sources including phase transformation, deformation twinning, and dislocations, giving rise to their exceptionally high hardenability and ductility. The atomic level heterogeneity in HEAs further gives rise to solid solution strengthening during dislocation motion. The concept of making atomic level heterogeneity can also be utilized in other metallic alloys for better hardenability and ductility.