Nakaoka and Palu introduced the notion of extriangulated categories by extracting the similarities between exact categories and triangulated categories. In this paper, we study cotorsion pairs in a Frobenius extriangulated category $\C$. Especially, for a $2$-Calabi-Yau extriangulated category $\C$ with a cluster structure, we describe the cluster substructure in the cotorsion pairs. For rooted cluster algebras arising from $\C$ with cluster tilting objects, we give a one-to-one correspondence between cotorsion pairs in $\C$ and certain pairs of their rooted cluster subalgebras which we call complete pairs. Finally, we explain this correspondence by an example relating to a Grassmannian cluster algebra.