Intra-operative ultrasound (US) is a popular imaging modality for its non-radiative and real-time advantages. However, it is still challenging to perform an interventional procedure under two-dimensional (2-D) US image guidance. Accordingly, the trend has been to perform three-dimensional (3-D) US image guidance by equipping the US probe with a spatial position tracking device, which requires accurate probe calibration for determining the spatial position between the B-scan image and the tracked probe. In this report, we propose a novel probe spatial calibration method by developing a calibration phantom combined with the tracking stylus. The calibration phantom is custom-designed to simplify the alignment between the stylus tip and the B-scan image plane. The spatial position of the stylus tip is tracked in real time, and its 2-D image pixel location is extracted and collected simultaneously. Gaussian distribution is used to model the spatial position of the stylus tip and the iterative closest point-based optimization algorithm is used to estimate the spatial transformation that matches these two point sets. Once the probe is calibrated, its trajectory and the B-scan image are collected and used for the volume reconstruction in our freehand 3-D US imaging system. Experimental results demonstrate that the probe calibration approach results in less than 1-mm mean point reconstruction accuracy. It requires less than 5 min for an inexperienced user to complete the probe calibration procedure with minimal training. The mockup test shows that the 3-D images are geometrically correct with 0.28°-angle accuracy and 0.40-mm distance accuracy.