Linear-optic photonic networks with multiple single-photon inputs are attracting attention due to their great potential for quantum computation, quantum communication, and quantum sensing. They are also essential for verifying quantum advantages via boson sampling schemes. The quantum coherence of generated multimode–multiphoton states is crucial for various applications. However, the coherence is invisible in the normally obtained photon number distributions, which strictly limits the efficiency of entanglement verification between multimode–multiphoton systems since the required resources for quantum state tomography increase exponentially as the number of photons/modes increases. In this paper, we report the experimental demonstration of direct and efficient verification of entanglement between two multimode–multiphoton systems (one photon in three modes and two photons in three modes) using just two sets of classical correlation tables with and without a discrete Fourier transformation of the optical modes, clearly demonstrating a dramatic reduction in the resources required for entanglement verification. Our experimental demonstration paves the way to understanding the coherence and entanglement of multi-partite systems, not only for photons but for other quantum resources with high-dimensional degrees of freedom.