In this paper, vibration behaviors of Fe nanowires are investigated by using the large-scale molecular dynamics (MD) simulations. It is observed that the vibration frequency of nanowires rises slightly and nonlinearly with the increase of initial actuation amplitude. Based on the atomic arrangement, a discrete spring-mass model is developed. Its nonlinear elastic relation is used to explain this phenomenon. In addition, Fe nanowires with different lengths and heights show different vibration properties in this work. The ratio between the length (L) and the height (h) of nanowires has a significant influence on vibration behaviors. The vibration properties of nanowires can be explained by the Euler–Bernoulli model when the ratio is relatively large, while they can be illustrated by the Timoshenko model when the ratio is relatively small.