The loop at the E-selectin binding site displayed open and close conformations observed in crystal structures before and after complexing with sialyl lewis x (sLex), respectively, and these different conformations were less studied and could affect the binding and dissociation of selectin/sLex that are essential for the recruitment of leukocytes and early inflammatory response. Hereby, we studied the roles of different loop conformations by performing molecular dynamics simulations, including adaptive steered MD simulations and energy calculations. Results suggested that the loop in the E-selectin binding site could switch from open to close conformation after the binding of sLex spontaneously, and the close conformation enhanced the binding by making sLex immersed slightly deeper in the binding site. Potential mean force calculations showed that more work was required for sLex to dissociate when the loop was in the close conformation, benefiting the formation of the catch bonds and prolonging the bonding lifetime by having more durable interactions between sLex and the loop residues in the rebinding step. This study provided atomic and dynamic details of the influence of the loop conformations on E-selectin/sLex interactions and further elucidated their mechanisms.