We first develop theories of differential rings of quasi-Siegel modular and quasi-Siegel Jacobi forms for genus two. Then we apply them to the Eynard-Orantin topological recursion of certain local Calabi-Yau threefolds equipped with branes, whose mirror curves are genus two hyperelliptic curves. By the proof of the Remodeling Conjecture, we prove that the corresponding open- and closed- Gromov-Witten potentials are essentially quasi-Siegel Jacobi and quasi-Siegel modular forms for genus two, respectively.