Copoly(Aspartic acid-Citric acid)(PAC) was prepared by copolymerizing aspartic acid and citric acid under microwave heating. Referring to the static scale inhibition method, the inhibition performance of PAC as CaCO3 scale inhibitor and the inhibition contrast and compatibility performance of PAC with HEDP were investigated. The morphology and structure of CaCO3 crystals and PAC were characterized by FTIR, NMR, AFM and XRD. The results showed that the synthesis of PAC was from aspartic acid and citric acid by the polymerization reaction of amidation and hydrolysis. PAC had excellent inhibition on CaCO3 scale, and its inhibition effects were superior to HEDP. The inhibition efficiency of PAC on CaCO3 reached 95.04% when the dose was 6.4 mg/L. PAC had better compatibility performance with HEDP, the inhibition effects of PAC/HEDP were superior to PAC. The analysis results of AFM and XRD showed that the morphology and structure of CaCO3 crystals were changed by PAC, transforming the most stable’s calcite into the most unstable’s vaterite.