In the field of joint surgery, the computer-aided design of knee prostheses suitable for the Chinese population requires a large quantity of anatomical knee data. In this study, we propose a new method that uses 3D Slicer software to automatically measure the morphological parameters of the distal femur. First, 141 femur samples were segmented from CT data to establish the femoral shape library. Next, balanced iterative reducing and clustering using hierarchies (BIRCH) combined with iterative closest point (ICP) and generalised procrustes analysis (GPA) were used to achieve fast registration of the femur samples. The statistical model was automatically calculated from the registered femur samples, and an orthopaedic surgeon marked the points on the statistical model. Finally, we developed an automatic measurement system using 3D Slicer software, and a deformable model matching method was applied to establish the point correspondence between the statistical model and the other samples. By matching points on the statistical model to corresponding points in other samples, we measured all other samples. We marked six points and measured eight parameters. We evaluated the performance of automatic matching by comparing the points marked manually with those matched automatically and verified the accuracy of the system by comparing the manual and automatic measurement results. The results indicated that the average error of the automatic matching points was 1.03 mm, and the average length error and average angle error measured automatically by the system were 0.37 mm and 0.63°, respectively. These errors were smaller than the intra-rater and inter-rater errors measured manually by two different surgeons, which showed that the accuracy of our automatic method was high. Taken together, this study established an accurate and automatic measurement system for the distal femur based on the secondary development of 3D Slicer software to assist orthopaedic surgeons in completing the measurements of big data and further promote the improved design of Chinese-specific knee prostheses.