A critical bottleneck that hinders major performance improvement in lithium-ion and sodium-ion batteries is the inferior electrochemical activity of their cathode materials. While significant research progresses have been made, conventional single-phase cathodes are still limited by intrinsic deficiencies such as low reversible capacity, enormous initial capacity loss, rapid capacity decay, and poor rate capability. In the past decade, layer-based heterostructured cathodes acquired by combining multiple crystalline phases have emerged as candidates with a huge potential to realize performance breakthrough. Herein, recent studies on the structural properties, electrochemical behaviors, and synthesis route optimizations of these heterostructured cathodes are summarized for in-depth discussions. Particular attention is paid to the latest mechanism discoveries and performance achievements. This review thus aims to promote a deeper understanding of the correlation between the crystal structure of cathodes and their electrochemical behavior, and offers guidance to design advance cathode materials from the aspect of crystal structure engineering.