Silk is extensively investigated in bone tissue engineering due to its extraordinary mechanical properties and ability to regulate biomineralization. Protein templates regulate biomineralization process through chemical interaction with ions. However, the effect of structural differences in silk fibroin on biomineralization has not been studied in detail. In this study, Antheraea pernyi silk fibroin (ASF) and Bombyx mori silk fibroin (BSF) fibers were used as templates to study the effect of silk species on biomineralization. The results showed that silk fibroin could induce the formation of calcium-deficient hydroxyapatite in simulated body fluid (SBF), and the SBF treatment resulted in the formation of silk I crystals. Compared with BSF, ASF exhibited a higher ability to induce mineralization, which may depend on the differences in hydrophilic amorphous fractions between ASF and BSF. The amorphous fractions of ASF contain more acidic amino acids, which can provide more nucleation sites in the initial stage of mineralization, resulting in faster mineralization process and more mineral deposits. This study decodes the key role of silk fibroin fractions on biomineralization, and provides deeper insights for the study of silk fibroin as biomineralization template and bone repair materials.