Localization is a key technology in Wireless Sensor Networks (WSN), while localization in three dimensional environments is very popular and will lead the future development of localization technology. We proposed an algorithm named LS3D DV-Hop (Layered structure based 3D DV-Hop), based on one of the typical range-free localization algorithm DV-Hop. We proposed a layered structure concept and projection based distance measuring method by analyzing the node deployment in buildings. Simulation results show that improved method has a better performance in robustness and stability in networks with few beacons.