We investigate the scattering processes of two photons in a one-dimensional waveguide coupled to two giant atoms. By adjusting the accumulated phase shifts between the coupling points, we are able to effectively manipulate the characteristics of these scattering photons. Utilizing the Lippmann-Schwinger formalism, we derive analytical expressions for the wave functions describing two-photon interaction in separate, braided, and nested configurations. Based on these wave functions, we also obtain analytical expressions for the incoherent power spectra and second-order correlation functions. In ...