This paper proposes a pipeline to automatically track and measure displacement and vibration of structural specimens during laboratory experiments. The latest Mask Regional Convolutional Neural Network (Mask R-CNN) can locate the targets and monitor their movement from videos recorded by a stationary camera. To improve precision and remove the noise, techniques such as Scale-invariant Feature Transform (SIFT) and various filters for signal processing are included. Experiments on three small-scale reinforced concrete beams and a shaking table test are utilized to verify the proposed method. Results show that the proposed deep learning method can achieve the goal to automatically and precisely measure the motion of tested structural members during laboratory experiments.