The stacking fault energy (SFE) effect on nanocrystalline metal deformation mechanisms has been extensively studied from dislocation and grain boundary perspectives. Compared to homogeneous nanocrystalline structures, the gradient nanograined (GNG) structure exhibits varied grain sizes, resulting in different SFE effects across regions during the hetero-deformation process. In this work, molecular dynamics (MD) simulation is conducted on GNG Cu-Ni binary alloys with incremental Ni concentration, to investigate the SFE effect at different deformation stages of the GNG structure. It is revealed that the elastic deformation stage shows a close relationship with alloy intrinsic property (e.g. elastic modulus) from Ni concentration variation, with neglectable SFE effect. Under the hetero-deformation stage, different from the homogeneous polycrystalline counterpart, the effect under high SFE condition is demonstrated from the overall dislocation density decline and the competition between the perfect and partial dislocations in the gradually varied grains across the GNG structure, which finally results in lower strain gradient, geometry necessary dislocation density, and a less effective hetero-deformation process. The active GB sliding and migration are found to offset this dislocation density decline in the sample with the relatively high SFE, which brings in higher GB stress concentration and larger GB free volume of the GNG structure. Besides, the GB relaxation across the GNG structure under the high strain rate tensile loading is also illustrated and discussed. The results further support the essential deformation mechanism underlying heterostructure materials.