Endoscopic video sequences provide surgeons with much structural information (e.g., vessels and neurovascular bundles) that guides them to accurately manipulate various surgical tools and avoid surgical risks. Unfortunately, it is difficult for surgeons to intuitively perceive these small structures with tiny pulsation motion on endoscopic images. This work proposes a new endoscopic video motion magnification method to accurately generate the amplified pulsation motion that can be intuitively and easily visualized by surgeons. The proposed method explores a new temporal filtering for Eulerian motion magnification method to precisely magnify the tiny pulsation motion and simultaneously suppress noise and artifacts in endoscopic videos. We evaluate our approach on surgical endoscopic videos acquired in robotic prostatectomy. The experimental results demonstrate that our proposed temporal filtering method essentially outperforms other filters in current video motion magnification approaches, while it provides better visual quality and quantitative assessment than other methods.