Due to their individual plastic deformation behavior and mechanistic performances, gradient nano-grained (GNG) metals have been identified as promising materials for application in advanced engineering applications. However, their plasticity mechanism has not been thoroughly investigated. Hence, in this work, molecular dynamics simulation was employed to characterize the atomistic behavior of copper GNG structures under tensile loading with different grain sizes (2–9 nm) at varied temperatures (100, 300, and 600 K). The results indicated that there existed a critical grain size value (6 nm) for the Hall–Petch and inverse Hall–Petch relationship. Besides, it was found that the high-temperature loading (600 K) negatively affected the plasticity-induced strengthening, while low-temperature loading induced outstanding plasticity-induced strengthening owing to the excessive strain hardening events. The details of plastic deformation from the perspective of grain boundary, deformation twining, stacking faults, and dislocations were analyzed and a thorough discussion was presented to elucidate the grain size and temperature effects on the plasticity mechanism.