Current marker-based facial motion capture methods might lose the target markers in some cases, such as those with considerable occlusion and blur. Manually revising these statuses requires extensive labor-intensive work. Thus, a robust marker tracking method that provides long-term stability must be developed, thereby simplifying manual operations. In this paper, we present a new facial marker tracking system that focuses on the accuracy and stability of performance capture. The tracking system includes a synthetic analysis step with the robust optical flow tracking method and the proposed Marker-YOLO detector. To illustrate the strength of our system, a real dataset of the performance of voluntary actors was obtained, and ground truth labels were given by artists for subsequent experiments. The results showed that our approach outperforms state-of-the-art trackers such as SiamDW and ECO in specific tasks while running at a real-time speed of 38 fps. The root-mean-squared error and area under the curve results verified the improvements in the accuracy and stability of our approach.