Phospholamban is an important protein with responsibility for regulating the activity of the sarcoplasmic reticulum Ca2+ pump through reversible phosphorylation. And its three-dimensional structure in living cell has been a focus of attention. In the current case, we summarized the investigations on phospholamban structure, and on this base, employed long time-scale molecular dynamics simulations to study its structure systematically. The first 22 residues from one chain of phospholamban in bellflower structure determined by NMR experiments, together with its phosphorylation at position 16 and mutation at position 9 were picked up as three different systems. By molecular dynamics simulations of 10 ns in the explicit solution surroundings, it was found that the 3–15 residues of the original structure retained their helix structures, while the phosphorylation and mutation had less probability to form helix structures. These structural changes might result in inhibition decrease to the sarcoplasmic reticulum Ca2+ pump, which is in accordance with previous experimental results.