A user-defined finite element subroutine (UEL) available in ABAQUS package is developed which can be used to simulate the micron-level size effect in large elastic-plastic deformation. Compared with traditional 8-node isoparametric elements,models formulated by quadrilateral area coordinate method are less sensitive to the mesh distortion. To quantify the size effect,the mechanism-based strain gradient plasticity is employed in the elastic-plastic constitutive model and is incorporated the quadrilateral area coordinate method. A numerical simulation is performed on the electro-polished nickel to verify correction of the new method. The micro-indentation experiment is done for the JX-2 pipeline steel (microstructure a dual phase consisting of ferrite and bainite). Through the comparison of the experimental and numerical results,it is shown that the new method outperforms the classical plasticity in the accuracy of predicting experimental results.