Atomic force microscopy (AFM) is originally used to observe the sample surface, and then extended to the area of nano-manipulation. It can be quite valuable in the further study of maneuvering nano-particles. Because of the influence of the tip morphology on the tip pushing direction, it is difficult to establish an effective operating model for stably manipulating nanoparticles with controllable manipulation results. To resolve this problem, the acting force of manipulating the nano-particle is analyzed firstly based on the least action principle. Then the influence of the contact point between the nano-particle and the tip is taken into account on the pushing direction, and manipulation of the nano-particle is modeled to predict its position after manipulation. Next, the model parameter is calibrated through several tests. Finally, the proposed model is verified by assembling the nano-structure. The experimental results illustrate that the model can effectively predict the nano-particle position after maneuvering, and can improve the manipulation efficiency.