Designing and synthesizing Si/C composites with a certain structure is an effective strategy to improve the performance of silicon anode materials for practical applications. Herein, we prepared Si/CNT composite microspheres with decent size uniformity and perfect spherical structure using droplet-microfluidics. The size and structure can be easily regulated by tuning the mass fraction of the precursor in the microfluidic device. The Si/CNT composite microspheres exhibited a narrow particle size distribution (coefficient of variation <15%) and a unique structure, where the silicon nanoparticles with an amorphous SiOx layer are uniformly encapsulated in a framework formed by CNTs (Carbon Nanotubes). In addition, the electrochemical performance of electrodes prepared with Si/CNT composite microspheres of different sizes and compositions was investigated, while the underlying mechanism is understood by both physical characterization and electrochemical measurement. This work lays the foundation for the rational design of Si/C composites and develops a new avenue for its commercialization.