In this paper, two kinds of asphalt rubber modifier pellets (ARP) and asphalt desulfurized rubber modifier pellets (ADRP) that can be directly injected were prepared by a screw extruder. Scanning electron microscopy (SEM) was employed to examine the internal microstructure of the two types of modifier pellets, and the storability were further evaluated. The rotational viscosity, high and low temperature rheological behaviors and fatigue properties of asphalt with two modifier pellets were investigated by rotational viscometer, dynamic shear rheometer (DSR), and bending beam rheometer (BBR), respectively. Infrared spectroscopy was used to explore the modification mechanism. The findings reveal that the content of desulfurized crumb rubber in the ADRP can be elevated to 80%, compared with 50% of crumb rubber in ARP. The surface of crumb rubber (CR) is smooth with prominent edges and corners, while desulfurized crumb rubber (DCR) reflects the rough surface with unclear edges and corners. Micro morphology verifies that asphalt and rubber manifest a good fusion phenomenon in ADRP. Incorporating anti-sticking agent lifts the collapse height of ARP and ADRP to nearly 9 cm and prevents their complete agglomeration, endowing their excellent storability. 20% DCR-MA reveals a Nf(5%) of 106,839 and superior fatigue resistance than 20% CR-MA, while it presents lower viscosity, rutting resistance, crack resistance and anti-aging performance. ADRP-MA demonstrates higher viscosity, rutting resistance, fatigue resistance and almost equivalent low-temperature performance than that of ARP-MA under the same dosage. Action mechanism of modified asphalt with both types of modifier pellets is regarded as a physical process. The modifier pellets prepared in this study reveal the merits of easy transportation, convenient direct injection, and wide application field.