Fast and accurate obstacle detection is essential for accurate perception of mobile vehicles’ environment. Because point clouds sensed by light detection and ranging (LiDAR) sensors are sparse and unstructured, traditional obstacle clustering on raw point clouds are inaccurate and time consuming. Thus, to achieve fast obstacle clustering in an unknown terrain, this paper proposes an elevation-reference connected component labeling (ER-CCL) algorithm using graphic processing unit (GPU) programing. LiDAR points are first projected onto a rasterized x–z plane so that sparse points are mapped into a series of regularly arranged small cells. Based on the height distribution of the LiDAR point, the ground cells are filtered out and a flag map is generated. Next, the ER-CCL algorithm is implemented on the label map generated from the flag map to mark individual clusters with unique labels. Finally, obstacle labeling results are inverse transformed from the x–z plane to 3D points to provide clustering results. For real-time 3D point cloud clustering, ER-CCL is accelerated by running it in parallel with the aid of GPU programming technology.