We investigate the single-photon transport properties in a hybrid waveguide quantum electrodynamics system, in which a one-dimensional waveguide is simultaneously coupled to a cavity and a driven Λ-type three-level atom. The cavity and the atom are also coupled to each other. We show that when the waveguide is coupled to the cavity and the atom at the same point, double electromagnetically induced transparency (EIT) can be observed from the system. The physical mechanism of the double EIT effect has been given by setting up the eigenstate structure for the whole system. When the waveguide is coupled to the cavity and the atom at different points, we demonstrate that the single-photon transmission spectra can be effectively controlled by adjusting the relative separation between the cavity and the atom. Moreover, this non-zero relative separation can lead to the occurrence of the controllable nonreciprocal scattering effect. These results have potential applications in realization of photonic coherent control.