The aims of this study were to explore the change of synovial fluid (SF) proteome in a knee osteoarthritis (KOA) rabbit model, and to provide a new target for the treatment of knee osteoarthritis at the proteomic level. Sixteen New Zealand rabbits were randomly and equally divided into two groups. Group A rabbits were subjected to right anterior cruciate ligament transection (ACLT), while group B rabbits were subjected to sham ACLT. Six weeks later, the proteomes of knee joint SF from group A and B rabbits were analyzed using a label-free quantitative proteomic analysis method. We extracted 944 relevant items from GO BlastGO2 for the 23 proteins differentially expressed between the two groups. The final annotation results were 23 protein sequences annotated by 462 GO items. According to the KEGG gene database of rabbit protein sequences, as well as annotation of the KO numbers of homologous/similar proteins to the relevant 64 KEGG pathways, we extracted the sequences of 16 significantly differently expressed proteins among the relevant 64 KEGG messages/metabolism pathways. These included adiponectin, pyruvate kinase, bisphosphoglycerate mutase, HtpG/heat shock proteins, hemoglobin subunit alpha-1 2, VCP (CDC48), 14-3-3 protein beta/theta/zeta, and ferritin heavy chain, whose levels were decreased in group A. The other proteins were fibrinogen alpha/beta/gamma chain, carboxylesterase 2, paraoxonase/arylesterase 1, apolipoprotein A-I, immunoglobulin heavy chain, and transferrin, whose levels were increased in group B. The identified differentially expressed proteins indicate the change of SF proteomic expression in KOA and may provide protein targets for treating this condition.