The efficient probing of spectral features of quantum many-body systems is important for characterising and understanding the structure and dynamics of quantum materials. In this work, we establish a framework for probing the excitation spectrum of quantum many-body systems with quantum simulators. Our approach effectively realises a spectral detector by processing the dynamics of observables with time intervals drawn from a defined probability distribution, which only requires native time evolution governed by the Hamiltonian without any ancilla. The critical element of our method is the engineered emergence of frequency resonance such that the excitation spectrum can be probed. We show that the time complexity for transition energy estimation has a logarithmic dependence on simulation accuracy, and discuss the noise e robustness of our spectroscopic method. We present simulation results for the spectral features of typical quantum systems, including quantum spins, fermions and bosons. We experimentally demonstrate how spectroscopic features of spin lattice models can be probed with IBM quantum devices.