As a new type of injectable biomaterials, functional microspheres have attracted increasing attention in tissue regeneration because they possess some advantageous properties compared to other biomaterials, including hydrogels. A variety of bio-inspired microspheres with unique structures and properties have been developed as cellular carriers and drug delivery vehicles in recent years. In this review, we provide a comprehensive summary of the progress of functional and biodegradable microspheres that have been used for tissue regeneration over the last two decades. First, we briefly introduce the biomaterials and general methods for microsphere fabrication. Next, we focus on the newly developed technologies for preparing functional microspheres, including macroporous microspheres, nanofibrous microspheres, hollow microspheres, core-shell structured microspheres, and surface-modified functional microspheres. After that, we discuss the application of functional microspheres for tissue regeneration, specifically for bone, cartilage, dental, neural, cardiac, and skin tissue regeneration. Last, we present our perspectives and future directions of functional microspheres as injectable carriers for the future advancement of tissue regeneration.