The calcium nitrate (Ca(NO3)2) waste generated from the production of nitrophosphate fertilizers brings about serious environment and human health issues. Using Ca(NO3)2 waste and ammonium bicarbonate (NH4HCO3) fertilizer as raw materials, higher-value spherical calcite mesocrystals have been synthesized via precipitation method. The synthesis conditions are optimized from the aspects of dispersant, crystal control agent and reaction temperature, and the mechanism that regulates the size and morphology of calcite is illustrated. The synthesized spherical calcite mesocrystals exhibit the small particle size of ca. 5 µm and high specific surface area of 84.44 m2/g. Under the dispersion effect of polyvinylpyrrolidone, the adsorption of crystal control agent citric acid on the calcite particles results in the formation of the spherical mesocrystal morphology. The yield of calcite in this process could reach 94.3%. Ca2+ ion remaining in the mother liquor are further removed in the form of CaCO3 by addition of calcium oxide, and a mixture of ammonium nitrate and a small amount of NH4HCO3 is obtained by concentrating the filtrate, which can be used as nitrogen fertilizers. This work provides a new insight into the low-cost synthesis of spherical calcite mesocrystals with the high specific surface area and the comprehensive utilization of Ca(NO3)2 waste.