Silicon has been intensively pursued as the most promising anode material for Li-ion batteries due to its high theoretical capacity of 3579 mAh/g. Micro-sized Si–C composites composed of nanoscale primary building blocks are attractive Si-based anodes for practical application because they not only achieve excellent cycling stability, but also offer both gravimetric and volumetric capacity. However, the effects of key parameters in designing such materials on their electrochemical performance are unknown and how to optimize them thus remains to be explored. Herein, the influence of Si nanoscale building block size and carbon coating on the electrochemical performance of the micro-sized Si–C composites is investigated. It is found that the critical Si building block size is 15 nm, which enables a high capacity without compromising the cycling stability, and that carbon coating at higher temperature improves the first cycle coulombic efficiency (CE) and the rate capability. Corresponding reasons underlying electrochemical performance are revealed by various characterizations. Combining both optimized Si building block size and carbon coating temperature, the resultant composite can sustain 600 cycles at 1.2 A/g with a fixed lithiation capacity of 1200 mAh/g, the best cycling performance with such a high capacity for micro-sized Si-based anodes.