We consider the quantum transport of multi-photon Fock states in a one-dimensional coupled QED cavity array (CQCA) as a scheme to probe the underlying strongly correlated (many-body) states of the system. To this end, we employ the Lippmann-Schwinger formalism within which an analytical form of the scattering matrix can be found. The latter is evaluated explicitly for the two photon-two site case, from which we calculate the scattering probabilities and auto-correlation functions. The results indicate that the underlying many body structure of the CQCAs can be directly inferred from the probe spectrum and output photon statistics. Our method goes beyond the usual case of using coherent light fields to drive the system and paves the way for CQCAs to serve as a quantum simulator of aspects of quantum transport in strongly correlated bosonic systems.