The peptidyl-prolyl imide bond cis/trans isomerization of Xaa-Pro motif in the peptide and protein plays an important role to influence their conformation and function. Here, a series of model peptides including phosphorylated and its unphosphorylated counterparts were designed and synthesized. Preliminary ¹H NMR experiments and molecular dynamics (MD) simulation were used to analyze the peptidyl-prolyl cis/trans imide bond isomerization. The data indicated that the side-chain O-phosphorylation of the Xaa residues preceding proline affected evidently the isomerization and thereby regulated the peptides conformations. The charges of the phosphate moiety as well as their steric effects might be the driving force for the conformational changes of these phosphopeptides. Moreover, the obtained most stable multiple configurations and their statistic cis/trans concentration distribution in MD simulation were basically consistent with the NMR experiments, which demonstrated that phosphorylation increased the cis conformation of the peptide and the maximum cis ratio is given while the phosphate group has no negative charge.