Over 300 polypeptide substrates can undergo catalysis by the constitutively active Ser/Thr kinase, human casein kinase 2 alpha (hCK2α). Quercetin, a naturally occurring polyphenolic compound, is well-known for inhibiting hCK2α, thereby regulating cellular signaling pathways. In this study, we crystallized the hCK2α-quercetin complex to elucidate the inhibitory mechanism of quercetin on hCK2α through the complex structure. The hanging drop vapor diffusion method was employed for crystallizing the hCK2α-quercetin complex, and the resulting crystal diffracted to a resolution of 2.11 Å. X-ray diffraction data analysis revealed that the crystal of the hCK2α-quercetin complex belonged to the P4₃2₁2 space group, with unit cell dimensions of a = b = 127.604 Å, c = 124.314 Å, and α = β = γ = 90.00°. In an initial density map, quercetin was bound well into hCK2α.