With the rapid interest in Geographic Information System (GIS) contents, a large volume of valuable GIS dataset has been distributed illegally by pirates, hackers, or unauthorized users. Therefore the problem focus on how to protect the copyright of GIS vector map data for storage and transmission. At this point, GIS security techniques focusing on secure network and data encryption have been studied and developed to solve the copyright protection and illegal copy prevention for GIS digital map. But GIS vector map data is very large and current data encryption techniques often encrypt all components of data. That means we have encrypted large amount of data lead to the long encrypting time and high complexity computation. This paper presents a novel selective encryption scheme for GIS vector map data protection to store, transmit or distribute to authorized users using K-means algorithm. The proposed algorithm only encrypts a small part of data based on properties of polylines and polygons in GIS vector map but it can change whole data of GIS vector map. Experimental results verified the proposed algorithm effectively and error in decryption is approximately zero.