The invention provides a shell-derived malic acid complex calcium and a preparation method thereof, relates to the green chemical preparation of marine biological materials and natural calcium nutrition enhancers, and belongs to the field of high-value utilization and recycling of shell resources and malic acid resources. Using shells as raw materials, acid solution is used to convert water-insoluble calcium salts in shells into water-soluble ionic calcium, solid-liquid separation to remove impurities, and then control the pH value, temperature, concentration and weight ratio of the filtrate, malic acid and calcium ions, complexation After precipitation of calcium ions, it is processed into calcium malate complex. The purity of this malic acid complexed calcium is ≥93%, of which the content of calcium ions is ≥17%, and the content of malic acid is ≥64%. The invention can significantly improve the purity, yield and quality of malic acid complexed calcium, has novel conception, rich raw materials, low cost, simple process, green environmental protection, easy implementation, great popularization, and can be used as a resource for shells and malic acid. High-value utilization and recycling have found new ways.