We report the design of a diamond-based honeycomb phononic network, in which a mechanical resonator couples to three distinct phononic crystal waveguides. This two-dimensional (2D) phononic network extends an earlier study on one-dimensional (1D) phononic networks with closed mechanical subsystems. With a special design for the phononic band structures of the waveguides, any two neighboring resonators in the 2D network and the waveguide between them can form a closed mechanical subsystem, which enables nearest neighbor coupling and at the same time circumvents the scaling problems inherent in typical large mechanical systems. In addition, the 2D network can be attached to a square phononic crystal lattice and be protected by the large band gap of the phononic crystal shield. Honeycomb phononic networks of spin qubits with nearest neighbor coupling can serve as an experimental platform for quantum computing and especially topological quantum error corrections.