Objective To investigate the expression level of semaphorin 3C (SEMA3C) and semaphorin 3F (SEMA3F) in synovial tissue of patients with rheumatoid arthritis (RA), and to analyze its correlation with clinical inflammatory markers and its clinical application value. Methods Knee joint synovial tissue specimens of 8 patients with RA and 8 patients with osteoarthritis (OA) were studied. The expression and distribution of SEMA3C, SEMA3F and tyrosine hydrogenase (TH) in synovial tissues were detected by immunohistochemistry. The mRNA and protein expression levels of SEMA3C and SEMA3F in synovial tissue were detected by real-time quantitative PCR and Western blot respectively. The correlations of SEMA3C and SEMA3F expression levels with erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), rheumatoid factor (RF), anti-cyclic citrullinated peptide antibody (ACPA), platelet count (PLT), plateletcrit (PCT), mean platelet volume (MPV), and platelet distribution width (PDW) were analyzed by Pearson method. Results Compared with those in synovial tissue of patients with OA, the distribution of SEMA3C and SEMA3F in synovial tissue of patients with RA was more extensive, while the expression of TH decreased. SEMA3C and SEMA3F mRNA and protein expressions in synovial tissue of patients with RA increased. Protein expression level of SEMA3C was negatively correlated with MPV and positively correlated with RF; protein expression level of SEMA3F was positively correlated with ESR and negatively correlated with PDW. Conclusion SEMA3C and SEMA3F are highly expressed in synovial tissue of patients with RA and correlated with the clinical inflammatory markers, which is expected to provide reference for the clinical evaluation of disease progression.