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Abstract We study the behavior of fermion spectral functions for the holographic topological Weyl and nodal line semimetals. We calculate the topological invariants from the Green functions of both holographic semimetals using the topological Hamiltonian method, which calculates topological invariants of strongly interacting systems from an effective Hamiltonian system with the same topological structure. Nontrivial topological invariants for both systems have been obtained and the presence of nontrivial topological invariants further supports the topological nature of the holographic semimetals.