The insightful understanding of phase transition in rare earth elements under shock compression is significant to the future development of materials science. In this work, a new reliable Finnis-Sinclair interatomic potential for hexagonal close-packed (HCP) single crystal yttrium (Y) is developed and validated. The potential reproduces the phase transition sequence of HCP → Sm-type (samarium-type) → DHCP (double hexagonal-close-packed) → FCC (face-centered-cubic) of Y observed in high-pressure experiments. Further, large-scale NEMD simulations are conducted to study shock compression behaviors of Y. For the [10−10]HCP shock direction, the HCP → Sm-type phase transition occurs via an intermediate metastable BCC structure, which is accomplished by atomic shuffles and shear. Then, a pure-shear along the [10−10]Sm-type direction transforms the Sm-type to DHCP structure. Besides, we find FCC phase can be generated by shifting the atoms at two layers in opposite <10−10> directions on {0001} planes in the DHCP lattice. Combined with the transition state theory, we confirm these transition pathways follow the minimum energy path. For shock along the [0001]HCP and [−12−10]HCP directions, the HCP → FCC phase transition is mediated by the amorphization which subsequently annihilates and turns to recrystallize to be FCC lattice. The results suggest that the uniaxial compression strain along the [0001]HCP and [−12−10]HCP directions hinders the formation of Sm-type and DHCP phases. Our findings provide essential insights into the phase transition behavior of Y under shock loading.