Recent experimental realization of one-dimensional (1D) spin-orbit coupling (SOC) for ultracold alkaline-earth(-like) atoms in optical lattice clocks opens a new avenue for exploring exotic quantum matter because of the strongly suppressed heating of atoms from lasers comparing with alkaline atoms. Here we propose a scheme to realize two-dimensional (2D) Rashba and three-dimensional (3D) Weyl types of SOC in a 3D optical lattice clock and explore their topological phases. With 3D Weyl SOC, the system can support topological phases with various numbers as well as types (I or II) of Weyl points. The spin textures of such topological bands for 2D Rashba and 3D Weyl SOC can be detected using suitably designed spectroscopic sequences. Our proposal may pave the way for the experimental realization of robust topological quantum matters and their exotic quasiparticle excitations in ultracold atomic gases.