The temperature effect on atomic deformation of nanotwinned Ni (nt-Ni) under localized nanoindentation is investigated in comparison with nanocrystalline Ni (nc-Ni) through molecular simulation. The nt-Ni exhibits enhanced critical load and hardness compared to nc-Ni, where perfect, stair-rod and Shockley dislocations are activated at (1$\mathop 1\limits^ -$1), ($\mathop 1\limits^ -$11) and (11$\mathop 1\limits^ -$) slip planes in nt-Ni compared to only Shockley dislocation nucleation at (1$\mathop 1\limits^ -$1) and ($\mathop 1\limits^ -$11) slip planes of nc-Ni. The nt-Ni exhibits a less significant indentation size effect in comparison with nc-Ni due to the dislocation slips hindrance of the twin boundary. The atomic deformation associated with the indentation size effect is investigated during dislocation transmission. Different from the decreasing partial slips parallel to the indenter surface in nc-Ni with increasing of temperature, the temperature-dependent atomic deformation of nt-Ni is closely related to the twin boundary: from the partial slips parallel to the twin boundary(~10K), to increased confined layer slips and decreased twin migration(300K~600K), to decreased confined layer slips and increased dislocation interaction of dislocation pinning and dissociation(900K~1200K). Dislocation density and atomic structure types through quantitative analysis are implemented to further reveal the above dislocation motion and atomic structure alteration. Our study helps to understand the temperature-dependent plasticity of twin boundary in nanotwinned material.