B-cell activating factor (BAFF) can binding to specific receptors and activate signaling pathways associated with B cell activation. Belimumab and tabalumab are anti-BAFF monoclonal antibodies, while belimumab was proved by FDA in 2011 as a targeted therapy for systemic lupus erythematosus (SLE) and showed better clinical effect than tabalumab. The combination modes of BAFF-belimumab complex and BAFF-tabalumab complex were simulated to better understand the reason for the difference of the inhibition effect between belimumab and tabalumab. The structures of belimumab and tabalumab were constructed by homology modeling.The combination mode of BAFF-belimumab complex was analyzed by molecular dynamics simulation, and the combination mode of BAFF-tabalumab complex was analyzed by protein-protein docking after molecular dynamics simulation. Both belimumab and tabalumab contacted with BAFF at the same hydrophobic center which the natural receptors of BAFF bind to. I51, F54, K58 D100, D101, L102, L103, P105 of belimumab heavy chain and R27, Y30, K49, S65 of belimumab light chain contribute to the BAFF-belimumab interaction mainly by hydrogen bond, salt bridge and hydrophobic effect. More important, Belimumab could contact with L83 of BAFF and produced a steric hindrance with the adjacent BAFF trimers, while tabalumab could not. Belimumab had better clinical effect than tabalumab mainly because it could bind to L83 of BAFF and affect the formation of BAFF 60-mer, in addition to inhibition of the interaction of BAFF with its receptors.