In this paper an extended Timoshenko beam element is developed for the investigation of size effect via finite element analysis. The surface effect derived from initial surface stress and surface elasticity is considered as external pressure in terms of the generalized Young-Laplace equation and the virtual displacement principle. We find the size effect highly relies on the geometrical model considered in numerical simulation. For a cantilever nanowire the stocky beam suddenly becomes strengthened provided the wire diameter is less than a critical size, while it is weakened for slender case. These abnormal changes of stiffness can be supported by static bending tests. This method will bring useful insight into the size effect and is of importance to some engineering applications like nanofabrication and nano sensors.