We theoretically investigate the quantum scattering of a single-photon pulse interacting with an ensemble of $Lambda$-type three-level atoms coupled to a one-dimensional waveguide. With an effective non-Hermitian Hamiltonian, we study the collective interaction between the atoms mediated by the waveguide mode. In our scheme, the atoms are randomly placed in the lattice along the axis of the one-dimensional waveguide, which closely corresponds to the practical condition that the atomic positions can not be controlled precisely in experiment. Many interesting optical properties occur in our waveguide-atom system, such as electromagnetically induced transparency (EIT) and optical depth. Moreover, we observe that strong photon-photon correlation with quantum beats can be generated in the off-resonant case, which provides an effective candidate for producing non-classical light in experiment. With remarkable progress in waveguide-emitter system, our scheme may be feasible in the near future.