Disclosed herein is a three-dimensional (3D) digital map system for implementing a navigation and ground collision preventing method using 3D terrain information. The 3D digital map system includes a terrain referenced navigation module configured to receive data from EGI (Embedded GPS/INS), a radio-altimeter (RALT) and a map database, corrects the data to perform accurate navigation computation, and outputs the corrected data, a collision avoidance warning module configured to generate a warning against collision of an aircraft with the ground or an obstacle using the corrected data, a 3D terrain database and an obstacle database, a terrain following module configured to generate a terrain following trajectory of the aircraft using the same information, and a Passive Ranging module configured to receive the 3D terrain database and line-of-sight (LOS) information of a target and calculate distance and position information of the target located on the ground.