This paper presents a technique to improve the accuracy of navigation of a satellite navigation system in the urban environment by effectively detecting and removing multipath signals in real time using 3D map information. To improve the satellite navigation accuracy, we designed a system that can implement an effective real-time ray-tracing calculation with 3D high-speed computation engine. In this process, objective multipath satellites can be identified and separated by collecting the actual satellite data around a complex urban environment and around the partial shadow areas during the satellite navigation. The Unity3D Engine ensures a real-time and efficient computing performance in large sized complex map environments and multiple access situations. By adapting the functionality of Unity3D, the GPU computation for satellite visibility is efficiently implemented in a complex map environment, resulting into the implementation of a real-time ray tracing function, even in a mobile platform. Consequently, the computation time for detecting a multipath signal with one set of satellite data is shortened. In addition, the root mean square error in estimating the horizontal position using the GPS L1 pseudorange least square navigation solution, which eliminates multipath signals, is reduced.