Based on the construction of polytope functions and several results about them in [LP], we take a deep look on their mutation behaviors to find a link between a face of a polytope and a sub-cluster algebra of the corresponding cluster algebra. This find provides a way to induce a mutation sequence in a sub-cluster algebra from that in the cluster algebra in totally sign-skew-symmetric case analogous to that achieved via cluster scattering diagram in skew-symmetrizable case by [GHKK] and [M]. With this, we are able to generalize compatibility degree in [CL] and then obtain an equivalent condition of compatibility which does not rely on clusters and thus can be generalized for all polytope functions. Therefore, we could regard compatibility as an intrinsic property of variables, which explains the unistructurality of cluster algebras. According to such cluster structure of polytope functions, we construct a fan $\mathcal{C}$ containing all cones in the $g$-fan. On the other hand, we also find a realization of $G$-matrices and $C$-matrices in polytopes by the mutation behaviors of polytopes, which helps to generalize the dualities between $G$-matrices and $C$-matrices introduced in [NZ] and leads to another polytope explanation of cluster structures. This allows us to construct another fan $\mathcal{N}$ which also contains all cones in the $g$-fan.