In this paper, nonlinear behaviors in the vibration 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 geometric nonlinearity is used to explain this phenomenon. In addition, Fe nanowires with different sizes 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 frequency changes linearly with h/L2 when the ratio is relatively large, while it changes nonlinearly when the ratio is relatively small.