Image-guided percutaneous needle puncture is a critical yet challenging clinical procedure, constrained by the high cognitive demand of mental model construction and manipulation of 3D anatomy via scrolling through 2D cross-sectional images. While virtual reality (VR) simulators provide a risk-free training platform, many focus on simulation fidelity but lack structured, self-directed learning frameworks. In this paper, we present PunctVR, a VR system that incorporates the instructional principles of scaffolding. PunctVR features a training mode employing a phased subgoal workflow and instructional guidance scaffolding, and an assessment-only test mode where both the workflow and enhanced 3D visualization are removed. We conducted a between-subject experiment with 16 physicians, comparing training using a baseline multiplanar reconstruction (MPR) view with a combined MPR + 3D visualization across two difficulty levels. Our test mode results indicate that all trainees significantly improved their performance after training. Furthermore, those who trained with the integrated 3D visualization achieved a greater reduction in puncture time in both easy and hard cases. These findings suggest that PunctVR effectively enhances procedural efficiency in simulated needle puncture training and provides important insights into how learning scaffolding can accelerate skill acquisition and retention for image-guided interventions.