Background For knee osteoarthritis (OA) treatment, it is important to correct the lower limb alignment including the foot. However, in the upright position, lower limb alignment is generally assessed from the body surface or radiographs, and it is a challenge to capture the exact characteristics of three-dimensional lower limb alignment. The purpose of the study was to measure lower limb alignment in patients with knee OA using upright computed tomography (CT) and radiography, and to identify features of knee joint deformity. Methods A total of 45 limbs in 25 patients with knee OA were enrolled. The subjects underwent both upright CT and radiography for the whole lower limb in the standing position. The joint angles were calculated on both images. The degree of knee OA was classified according to Kellgren-Lawrence (KL) grade by referring to radiography, which is mainly based on the degree of articular cartilage loss and severity of osteophytes, and the characteristics or correlation between knee and ankle joint in each group was investigated. Results In KL-I, there was an association between varus of the knee joint and internal rotation of the talocrural joint ( r = 0.76, P < 0.05). In KL-II, there was an association between varus of the knee joint and eversion of the subtalar joint ( r = 0.63, P < 0.05) and talocrural joint ( r = − 0.65, P < 0.05). In KL-III, there was an association between varus of the knee joint and internal rotation of the subtalar joint ( r = − 0.62, P < 0.05), and in KL-IV, there was an association between varus of the knee joint and internal rotation of the subtalar joint ( r = − 0.58, P < 0.05). Conclusions The lower limb alignment of patients with knee OA in the standing position was found that as knee OA worsened, it became apparent that compensatory knee joint alignment depended on the ankle joint rather than the subtalar joint. The results may help in the rehabilitation of patients with knee OA, since the ankle joint alignment has a significant impact on the knee joint during coarse movements involving load.