Graph states are entangled resource states for universal measurement-based quantum computation. Although matter qubits such as superconducting circuits and trapped ions are promising candidates to generate graph states, it is technologically hard to entangle a large number of them due to several types of noise. Since they must be sufficiently cooled to maintain their quantum properties, thermal noise is one of major ones. In this paper, we show that for any temperature T , the fidelity G|ρT |G between an ideal graph state |G at zero temperature and a thermal graph state ρT , which is a graph state at temperature T , can be efficiently estimated by using only one measurement setting. A remarkable property of our protocol is that it is passive, while existing protocols are active, namely they switch between at least two measurement settings. Since thermal noise is equivalent to an independent phase-flip error, our estimation protocol also works for that error. By generalizing our protocol to hypergraph states, we apply our protocol to the quantum-computational-supremacy demonstration with instantaneous quantum polynomial time circuits. Our results should make the characterization of entangled matter qubits extremely feasible under thermal noise.