Nanocrystalline metals possessing excellent mechanical strength have great potential to replace traditional metal materials as structural materials, but their poor resistance to creep deformation seriously restricts their engineering applications at high temperatures. The high-temperature creep behavior of nanocrystalline Ni with different volume fractions of initial vacancies ranging from 0% to 10% was studied systematically by molecular dynamics simulation in this study. The results showed that the steady-state creep displacement first increased and then decreased with increasing initial vacancy concentration, reaching the maximum when the initial vacancy concentration was 6%. The microstructural characteristics, such as quantity increment and distribution of the vacancies, the number and types of dislocations, and shear strain distribution during creeping, were analyzed in detail. The deformation-induced vacancies formed at the grain boundary (GB) in the initial creep stage, and their variation trend with the initial vacancy concentration was consistent with that of the creep displacement, indicating that the initial vacancy-dependent high-temperature creep behavior of nanocrystalline Ni was mainly determined by the rapidly increasing number of vacancies at the GB in the initial creep stage. Afterwards, the deformation-induced, vacancy-assisted 1/6{112} Shockley partial dislocation activities dominated the creep deformation of nanocrystalline Ni in the steady-state creep stage. The results can provide theoretical support for expanding the application of nanocrystalline metals from the perspective of crystal defect engineering.