We investigate coherent control of a single atom interacting with an optical bipartite lattice via a combined high-frequency modulation. Our analytical results show that the quantum tunneling and dynamical localization can depend on phase difference between the modulation components, which leads to a different route for the coherent destruction of tunneling and a convenient phase-control method for stabilizing the system to implement the directed transport of atom. The similar directed transport and the phase-controlled quantum transition are revealed for the corresponding many-particle system. The results can be referable for experimentally manipulating quantum transport and transition of cold atoms in the tilted and shaken optical bipartite lattice or of analogical optical two-mode quantum beam splitter, and also can be extended to other optical and solid-state systems.