Following our previous work \cite{HLY}, we introduce the notions of partial seed homomorphisms and partial ideal rooted cluster morphisms. Related to the theory of Green's equivalences, the isomorphism classes of sub-rooted cluster algebras of a rooted cluster algebra are corresponded one-by-one to the regular $\mathcal D$-classes of the semigroup consisting of partial seed endomorphisms of the initial seed. Moreover, for a rooted cluster algebra from a Riemannian surface, they are also corresponded to the isomorphism classes of the so-called paunched surfaces.