3D flower-like MnCO3 microcrystals have been prepared via a facile hydrothermal method with the addition of sodium citrate (Na3Cit). The microstructures of the prepared microcrystals were characterized through X-ray diffraction (XRD), scanning electron microscope (SEM), thermogravimetric analysis (TGA), fourier transform infrared spectroscopy (FTIR) and N2 adsorption. Moreover, a mechanism for the morphology evolution of 3D flower-like MnCO3 microcrystals was also discussed in detail. Using the obtained 3D flower-like MnCO3 microcrystals as anode for lithium ion batteries and a series of tests including charge-discharge test, cycling ability, rate performances, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were carried out. The results show that 3D flower-like MnCO3 microcrystals can be obtained by varying the reaction time and the dosage of Na3Cit at the hydrothermal temperature of 180°C, and the suitable hydrothermal reaction time and the dosage of Na3Cit for the 3D flower-like MnCO3 microcrystals are 12h and 3mmol, respectively. The electrochemical measurements indicate that 3D flower-like MnCO3 microcrystals exhibit specific capacity of 384mAhg−1 at 0.2C after 200 cycles, showing the significantly enhanced cycling performance than that of the obtained spherical MnCO3 microcrystals.