Introduction: Knee osteoarthritis (KOA) is characterized by a degenerative change of knee cartilage and secondary bone hyperplasia, resulting in pain, stiffness, and abnormal walking gait. Long-term chronic pain causes considerable cortical plasticity alternations in patients. However, the brain structural and functional alterations associated with the pathological changes in knee joints of end-stage KOA patients remain unclear. This study aimed to analyze the structural and functional connectivity alterations in end-stage KOA to comprehensively understand the main brain-associated mechanisms underlying its development and progression. Methods: In this study, 37 patients with KOA and 37 demographically matched healthy controls (HCs) were enrolled. Alternations in gray matter (GM) volume in patients with KOA were determined using voxel-based morphometry. The region with the largest GM volume alteration was selected as the region of interest to calculate the voxel-wise resting-state functional connectivity (rs-FC) in the two groups. Pearson's correlation coefficient was used to analyze the correlation between clinical measures and GM volume alternations in patients with KOA. Results: Compared with HCs, patients with KOAs exhibited significantly decreased GM volumes in the left middle temporal gyrus (left-MTG) and the left inferior temporal gyrus. Results of the voxel-wise rs-FC analysis revealed that compared with HCs, patients with KOA had decreased left-MTG rs-FC to the right dorsolateral superior frontal gyrus, left middle frontal gyrus, and left medial superior frontal gyrus. GM volume in the left-MTG was negatively correlated with the Western Ontario and McMaster Universities Arthritis Index in patients with KOA (r = −0.393, p = .016). Conclusion: Structural remodeling and functional connectivity alterations may be one of the central brain mechanisms associated with end-stage KOA.