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Catheter-based intervention procedures contain complex maneuvers, and they are often performed using fluoroscopic guidance assisted by 2D and 3D echocardiography viewed on a flat screen that inherently limits depth perception. Emerging mixed reality (MR) technologies, combined with advanced rendering techniques, offer potential enhancement in depth perception and navigational support. The study aims to evaluate a MR-based guidance system for the atrial septal puncture (ASP) procedure utilizing a phantom anatomical model. A novel MR-based guidance system using a modified Monte Carlo-based rendering approach for 3D echocardiographic visualization was introduced and evaluated against standard clinical 3D echocardiographic display on a flat screen. The objective was to guide the ASP procedure by facilitating catheter placement and puncture across four specific atrial septum quadrants. To assess the system’s feasibility and performance, a user study involving four experienced interventional cardiologists was conducted using a phantom model. Results show that participants accurately punctured the designated quadrant in 14 out of 16 punctures using MR and 15 out of 16 punctures using the flat screen of the ultrasound machine. The geometric mean puncture time for MR was 31 s and 26 s for flat screen guidance. User experience ratings indicated MR-based guidance to be easier to navigate and locate tents of the atrial septum. The study demonstrates the feasibility of MR-guided atrial septal puncture. User experience data, particularly with respect to navigation, imply potential benefits for more complex procedures and educational purposes. The observed performance difference suggests an associated learning curve for optimal MR utilization.