Natural biominerals are usually composite materials produced through mineralization of inorganic crystals within an organic matrix. Silk fibroin is known to be capable of directing the nucleation and growth of hydroxyapatite crystals. Here, we used silk films as the substrate to induce the mineralization of calcium phosphate. We show that the silk fibroin in solution could induce the formation of monetite crystals with a hierarchical structure, which are assembled by well aligned single crystals of monetite. In addition, we show that silk fibroins are incorporated inside the crystals. Therefore, the self-assembly of silk fibroin during the crystallization process is critical for the formation of such hierarchical structures.