Biochemical fulvic acid (BFA), produced by organic wastes composting, is the complex organic matter with various functional groups. A novel modified biochemical fulvic acid (MBFA) which possessed stronger chelating ability had been synthesized by the grafting copolymerization of BFA and acrylic acid (AA). Results showed that MBFA effectively inhibited the crystallization of calcium phosphate and increased the concentration of phosphate in water solution. The optimum reaction conditions optimized by Box–Behnken design and response surface methodology were reaction temperature 69.24 °C, the mass of monomer to fulvic acid ratio 0.713, the initiator dosage 19.78%, and phosphate crystal-inhibition extent was 96.89%. IR spectra demonstrated AA was grafted onto BFA. XRD data and SEM images appeared the formation and growth of calcium phosphate crystals was effectively inhibited by MBFA.