MXenes (transition metal carbides and nitrides) have experienced exponential growth over the last two decades, thanks to their excellent physical, chemical, and mechanical properties. Intriguing properties like high conductivity, wear, and corrosion resistance while maintaining flexibility are the strong motivation behind the exploration of MXenes. Moreover, the large surface area and unique layered structure enhance the functionality of multilayer-MXene heterostructures and hybrids. This paper reviews the synthesis chemistry, structure properties of multilayer MXenes, and their multifunctional applications. MXene synthesis under different conditions, their hybrids and composites, intercalation, and structural geometries are discussed. The electrical, mechanical, optical, and magnetic properties of MXenes are briefly presented. Recent progress and development in MXene-based heterostructures and nanohybrids for supercapacitors, batteries, environmental and water treatment, antibacterial and tissue engineering, and electromagnetic absorption and shielding are systematically discussed. Finally, research challenges and a perspective in this specified area are addressed for potential developments.