Background: The implementation of lateral ventricle puncture (LVP) operation is challenging due to the complex anatomy structure of human brains. Surgical simulator has been proved to be effective in surgical training. However, few works consider the integration of visual and haptic feedback. Methods: Aim at achieving a realistic haptic interaction, this paper proposes a haptic-based virtual reality (VR) simulator for the LVP operation. In this simulator, we first reconstruct the three-dimension (3D) model of human brains for tissue/ instrument interaction. Then a preoperative planning method based on geometry analysis is introduced to find the feasible entry point of LVP operation. A hierarchical bounding-box collision detection approach is proposed to render haptic feedback that is transferred to humans. Finally, a set of experiments on the proposed simulator and 3D printed models of human brains is carried out. Results: Two sets of experiments are conducted to evaluate the effectiveness of the proposed haptic-based simulator: experiments in the simulator and experiments on a 3D printed brain model. The proposed simulator allows neurosurgeons to train the LVP operation by visualizing the 3D virtual human brain and feeling realistic haptic feedback. Conclusions: We demonstrated that the proposed haptic-based VR simulator can improve the performance of the LVP operation effectively and reduce the operation time.