Understanding 3D scene dynamics in minimally invasive surgery (MIS) is a fundamental step toward physically intelligent and autonomous surgical systems. However, existing public datasets offer limited scalability and diversity in real-world clinical scenarios. Moreover, annotations typically focus on either tissue or instruments alone, overlooking tool-tissue interactions. This gap limits applications such as augmented reality guidance and autonomous surgery driven by vision-language-action (VLA) models or world models, which demand large-scale, high-quality 3D supervision. In this work, we construct SurgTAP-3D, a large-scale in-vivo pseudo-3D surgical motion tracking dataset and benchmark, comprising 520K frames, 4,549 action clips, and 1.4M 2D/3D point trajectories from diverse robotic and manual procedures under unified action categories. To make annotation scalable, we design a unified framework for surgical 3D point tracking that converts uncalibrated monocular surgical videos into structured 4D annotations through contact-region prompting, active-tool segmentation, dynamic bundle adjustment, and global 4D refinement. This pipeline adapts foundation priors to surgical videos and produces temporally consistent trajectories, pseudo-scale geometry, camera poses, and instrument masks. The dataset captures realistic challenges inherent to surgical environments, including occlusions, smoke, bleeding, and rapid instrument motion. We establish a comprehensive benchmark on SurgPose, SurgT, and STIR, covering both instrument and tissue tracking. We demonstrate instrument displacement estimation, deformable surface reconstruction, and foundation-model fine-tuning. Extensive experiments and analysis demonstrate the effectiveness of our dataset and annotation framework for 3D surgical point tracking, reconstruction, and surgical action understanding. Homepage: https://wrld.github.io/surgtap-3d/

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