Based on the symmetric, asymmetric atom-photon couplings and the phase difference between two separated atoms, single-photon transport properties in an optical waveguide coupled with two separated two-level atoms are theoretically investigated. The transmission and reflection amplitudes for the single-photon propagation in such a hybrid system are deduced via a real-space approach. Several new phenomena such as phase-coupled induced transparency, single-photon switches, symmetric and asymmetric bifrequency photon attenuators are analyzed. In addition, the dissipation effect of such a hybrid system is also discussed.