Abstract: The spatial registration is a key technology in the image guided neurosurgery and the determination of correspondence position between points of two point sets is also an essential part.A novel image registration method based on balanced VP-Tree（Vantage Point Tree） is proposed，which improves the classical VP-Tree structure’s balance and enhances the efficiency of searching point-pair.Firstly，SVD（Single Value Decomposition） algorithm is applied for coarse registration.Secondly，ICP（Iterative Closest Point） algorithm is applied for accurate registration，in which VP-Tree structure is used to find closest point.An experiment shows that the registration is suitable for clinical application，which can be implemented conveniently，quickly，robustly and accurately（errors are limited in 1 mm）.