In order to predict the structure and B cell liner epitopes of sesame allergen Ses i 3， the bio-information Editseq software of DNAStar， the network server-SOMPA and The BepiPred 1.0 Server were used to predicted the antigenicity， hydrophilicity， surface probability， flexibility and secondary structure. The B-cell prediction epitope was synthetically analyzed. The tertiary structure of Ses i 3 protein was successfully built by homology modeling with SWISS-MODEL and evaluated by the Ramachandran software for stability. Results indicated that B-cell liner epitopes had the high probability in the regions of SESKDP， RQKHQGEHG， NRKSP， QHG， YQREKGRQDDDNPTDPEKQY， RRQG， KYREQQGREGGRGE， EGR， EQGR， RQDR， ENP， RHE， ESK， RPTH， ASQ， SRSRGSYQGETRGRP， ANNNE， SRSQQ， GPRQQQQGR. Homologous modeling with 5e1r.2 as the template successfully constructed the tertiary structure of sesame allergen Ses i 3， and Ramachandran's evaluation showed that the protein model was conformational stable. These results provide a basis for the preparation of specific antibody peptides and the detection of allergens.