Background Risk factors for the severity of patellofemoral osteoarthritis (PFOA) are poorly understood. This research aims to evaluate the association between patellofemoral joint (PFJ) morphology and alignment with the radiographic severity of PFOA. Methods A retrospective analysis of CT scan and lateral radiograph data were acquired in patients with PFOA. The radiographic grade of PFOA and tibiofemoral osteoarthritis (TFOA), lateral and medial trochlear inclination angle, sulcus angle, and the Wiberg classification of patella morphology, the congruence angle, patellar tilt angle, and lateral patellar angles, and tibial tubercle trochlear groove distance (TT-TG) and patella height (i.e., Caton-Deschamps index) were assessed using CT scans and sagittal radiographs of the knee. All the PFJ morphology and alignment data were divided into quarters, and the relationships between each of these measures and the severity of PFOA were investigated. Results By studying 150 patients with PFOA, we found a U-shaped relationship between the Caton-Deschamps index and the severity of PFOA (P < 0.001). A lower value of sulcus angle and lateral patellar angle, a higher value of congruence angle, and type III patella were associated with more severity of lateral PFOA. Compared with the highest quarter of each measure, the adjusted odds ratios (OR) of the severity of PFOA in the lowest quarter of sulcus angle, lateral patellar angle, and congruence angle; and type I patella was 8.80 (p = 0.043), 16.51 (P < 0.001), 0.04 (P < 0.001), and 0.18 (p = 0.048) respectively. Conclusions Extreme value of patella height, a higher value of lateral patellar displacement and lateral patellar tilt, lower value of sulcus angle, and type III patella were associated with more severity of PFOA.