Objective To study the relationship of the tibial plateau subchondral trabecular bone (STB) microstructure and the cartilage degeneration with the lower limb alignment based on individual trabecula segmentation (ITS) and histology analysis in knee osteoarthritis (OA). Methods Hip-knee-ankle (HKA) angles were measured on the full-length lower extremity films of patients before total knee arthroplasty (TKA). The tibial plateau excised from the TKA were collected for micro-CT scanning and ITS analysis. The cartilage degeneration was evaluated by histology. The relationship between the HKA angle and the changes in microstructural parameters of STB and cartilage degeneration were analyzed. ResultsThe plate, rod and axial bone trabecular volume fraction (BV/TV, pBV/TV, pBV/TV), ratio of trabecular plate versus rod (P/R), plate trabecular number density (pTb.N), plate trabecular thickness (pTb.Th), trabecular plate surface area (pTb.S), trabecular rod length (rTb.L), and plate-plate and plate-rod junction density (P-P Junc.D, P-R Junc.D) of the subchondral bone of the tibial plateau were significantly related to the cartilage degeneration OARSI score and the HKA angle. The greater the deviation of the lower limb alignment, the greater the number of subchondral trabeculae, the thicker the trabeculae, the greater the bone mass, the stronger the connectivity, especially the plate trabeculae on the affected side of tibial plateau, and the higher the OARSI score of cartilage degeneration. Conclusions Abnormal lower limb alignment may cause abnormal microstructure of the plate and rod STB of the tibial plateau by changing the stress distribution of the knee, especially the significant increase and thickening of the plate trabecular and axial trabecular bone, which may be an important risk factor that further aggravates the degeneration of articular cartilage and the progress of OA. Therefore, lower limb alignment correction with surgical intervention and improving STB with bone metabolism agents may efficiently contribute to preventing cartilage damage and mitigate OA progression.