Nanoparticles-assembled Co3O4 microspheres with different primary particle size are synthesized via a facile one-step ultrasonic spray pyrolysis process, using CoCl2·6H2O as precursor. The as-synthesized Co3O4 powders are directly used as anode material for Li-ion batteries without further calcinations. The primary particle size is tuned by controlling the spray pyrolysis temperature and its effects on the electrochemical performance of the prepared samples are systemically investigated. The results reveal that primary particles size exerts significant effect on the initial coulombic efficiency, specific capacity and rate performance. In addition, we find that the temperature of powder collector strongly influences the chlorine content in the products, which is resulted from the chloridization of Co3O4 by gaseous HCl from the off-gas. A simple and effective strategy is proposed to prevent the chloridization reaction. The sample with the smallest primary particle size and low Cl content shows the highest initial coulombic efficiency of 73% and a high reversible capacity of 1340mAhg−1 after 50 cycles at a current density of 200mAg−1.