High-performance, Si-based three-dimensional (3D) microbattery systems for powering micro/nanoelectromechanical systems and lab-on-chip smart electronic devices have attracted increasing research attention. These systems are characterized by compatible fabrication and integratibility resulting from the silicon-based technologies used in their production. The use of support substrates, electrodes or current collectors, electrolytes, and even batteries used in 3D layouts has become increasingly important in fabricating microbatteries with high energy, high power density, and wide-ranging applications. In this review, Si-based 3D microbatteries and related fabrication technologies, especially the production of micro-lithium ion batteries, are reviewed and discussed in detail in order to provide guidance for the design and fabrication.