The invention provides a calcium phosphate nanoparticle-ionic complementary peptide composite hydrogel and a preparation method thereof. The composite hydrogel is an assembly formed by self-assembling of electronegative ionic complementary peptide with excess amino acid residues, and calcium phosphate nanoparticles are synthesized on the surface of the assembly in situ. The composite hydrogel is formed by compounding the self assembly of the ionic complementary peptide and the calcium phosphate nanoparticles and is effectively improved in strength; moreover, the assembly of the ionic complementary peptide can restrict in-situ growth of the calcium phosphate nanoparticles on the surface of the assembly and effectively control the particle size distribution of the calcium phosphate nanoparticles.