Objective To compare the difference between CT measured and MRI measured femoral posterior condylar angle (PCA) in varus osteoarthritis knees. Methods The CT data of lower-extremity and MRI data of involved knees in 71 patients (73 varus osteoarthritis knees) who underwent primary TKA at Department of Orthopedic Surgery,Jiangsu Province Hospital from November 2018 to February 2020 was retrospected in our study. The CT and MRI images were used to measure PCA respectively. MRI images were also used to measure the cartilage thickness of femoral posterior condyles and distal femoral condyles. At the same time, the thickness of femoral posterior condylar cartilage of specimens was also measured. The measurement results were compared and analyzed for correlation Results The PCA-CT (4.09±1.39)°was significant larger than PCA-MRI (2.25±1.01)°(P<0.01). The MRI measured cartilage thickness of medial posterior condyle (1.9±0.6)mm and cartilage thickness of lateral posterior condyle (2.8±0.5)mm, MRI measured cartilage thickness of medial distal femoral condyle (1.3±0.4)mm and cartilage thickness of lateral distal femoral condyle(2.5±0.4)mm, cartilage thickness of medial posterior condyle of specimens(1.9±0.6)mm and cartilage thickness of lateral posterior condyle of specimens(2.8±0.6)mm all presented significant difference between each other. Also, Pearson correlation analysis results showed that: if 2mm cartilage thickness difference exists between medial and lateral posterior condyle, almost 3° external malrotation was found between PCA-CT and PCA-MRI. Conclusions Cartilage wear of medial posterior condyle commonly occurs in varus knee osteoarthritis and this has an impact on the rotational alignment of femoral component. Significant differences exist in preoperative measurements of MRI and CT, and orthrpedic surgeons must take this difference into consideration when making preoperative planning.