Physicians use Capsule Endoscopy (CE) as a noninvasive and non-surgical procedure to examine the entire gastrointestinal (GI) tract for diseases and abnormalities. A single CE examination could last between 8 to 11 hours generating up to 80,000 frames which is compiled as a video. Physicians have to review and analyze the entire video to identify abnormalities or diseases before making diagnosis. This review task can be very tedious, time consuming and prone to error. While only as little as a single frame may capture useful content that is relevant to the physicians' final diagnosis, frames covering the small bowel region alone could be as much as 50,000. To minimize physicians' review time and effort, this paper proposes a novel unsupervised and computationally efficient temporal segmentation method to automatically partition long CE videos into a homogeneous and identifiable video segments. However, the search for temporal boundaries in a long video using high dimensional framefeature matrix is computationally prohibitive and impracticable for real clinical application. Therefore, leveraging both spatial and temporal information in the video, we first extracted high level frame features using a pretrained CNN model and then projected the high-dimensional frame-feature matrix to lower 1-dimensional embedding. Using this 1-dimensional sequence embedding, we applied the Pruned Exact Linear Time (PELT) algorithm to searched for temporal boundaries that indicates the transition points from normal to abnormal frames and viceversa. The key novelty of this work is in three (3) folds -first, the automated detection of temporal boundaries in long CE video has not been previously considered. Secondly, the reduction in the computational cost of the temporal boundary detection search by using a lower dimensional frame feature embedding; and lastly, the entire temporal segmentation of the CE videos requiring no supervision from medical expert is a new concept. The output of our model can be easily integrated into any CE video summarization model where physicians only need to review a selected sample frame from each video segment. We experimented with multiple real patients' CE videos and our result showed PCA was superior in capturing the transition between pair of normal and abnormal frames in the video. We also bench-marked with expert provided label, and our system achieved an AUC of 66% on multiple test videos.