This paper presents the influence of temperature on microstructure and phase transition when heating 3000 nano-iron and bulk-iron particles at a temperature of 300 K, 500 K, 700 K, 900 K, 1100 K. 1300 K, 1500 K. 1700 K, 1900 K and 2100 K using the molecular dynamics (MD) simulation method. The models were applied in the Sutton-Chen embedded position with the bulk-iron models with the periodic boundary condition and the nano-iron models with aperiodic boundary conditions. The microstructure characteristics of the models were analyzed by using the radial distribution function (PRDF), the average density, the coordination number, the average coordination number and the phase transition temperature of the models was determined based on the temperature dependence of average energy. The results show that temperature influences microstructure aod phase transition of the models. For nano-iron models, the phase transition temperature is about 1398 K while it is about 1750 K for bulk-iron models. In addition, the microstructure characteristics of the surface layer and the core layer of the models are different when the models are at different temperatures.