Morphological anisotropic engineering is powerful to synthesize metal‐organic frameworks (MOF) with versatile physicochemical properties for diverse applications ranging from gas storage/separation to electrocatalysis and batteries, etc. Herein, we developed a carbon substrate guided strategy for facet‐anisotropic growth of Fe‐THBQ (tetrahydroxy‐1,4‐benzoquinone) frameworks, which is built with cubic Fe octamer bridged by two parallel THBQ ligands along three orthogonal axes, extending to a three‐dimensional (3D) framework with pcu‐e network topology. The electronegative O‐containing functional groups on carbon surfaces compete with THBQ linkers to interact with the unsaturated coordinated Fe cations on the {111} facets and selectively inhibit crystal growth along the <111> direction. The morphology of Fe‐THBQ evolves from thermodynamically favored truncated cube to cuboctahedron depending on the O‐containing functional groups on carbon substrate. The Fe‐THBQ with varied morphologies exhibits facet‐dependent performances for lithium storage. This work will shed lights on morphology modulation of MOFs for promising applications.