Phosphate removal from eutrophic lakes has caused wide concern in the world, while an effective process is still lacking. A novel synthetic magnesium carbonate with spherical flower-like structure (MCSF) was prepared. Its performance for phosphorus adsorption from a eutrophic lake by in situ magnesium phosphate formation was tested and characterized. The effect of initial phosphorus concentration, adsorption time, adsorption dose, temperature, ionic strength and pH on phosphorus adsorption by MCSF was investigated. Results showed that higher initial phosphorus concentration and longer adsorbing time could improve the adsorption capacity. The maximum sorption capacity was 143.27 mg/g under initial pH value 7.0. The phosphate adsorption process was fitted with the Langmuir isotherm model and pseudo-second-order model. Thermodynamic parameter values revealed that the sorption process at 298–318 K was spontaneous and endothermic. The X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) characterization of MCSF revealed that electrostatic attraction and chemical conversion were the major contributors for phosphate adsorption. MCSF releases magnesium ions from its surface and rapidly combines with phosphate to form insoluble magnesium phosphate precipitate. The prepared MCSF has the potential to be used for the restoration of eutrophic lakes by removing phosphate with higher adsorption capacity.