The modification of CaCO3 crystal growth by synthetic L-Ser(PO3H2) and L-Thr(PO3H2) containing polypeptides is described. The amino acids Gly, L-Glu, L-Asp, L-Ser, L-Ala, and L-Lys induced rhombohedral calcite with a rough surface. Dipeptides, Xaa-L-Ser(PO3H2) (Xaa = Gly, L-Glu, L-Asp, L-Ser, L-Ala and L-Lys) induced vaterite crystals in the lower [Ca2+]. On the other hand, L-Ser(PO3H2)-containing polypeptides formed spherical vaterite and fibrous calcite. The characteristic helical calcite was found in the presence of copoly[L-Ser(PO3H2)75L-Asp25] or poly[L-Ser(PO3H2)3–L-Asp]. Fibrous calcite, spherical vaterite, and helical calcite crystals were subjected to XRD and EDX analysis. XRD revealed the specific faces of these crystals. EDX spectra and surface analysis visualized the localization of the polypeptides and CaCO3 components. Together with TEM and SAED data, we propose hypothetical growth mechanisms for the fibrous and helical calcite crystals.