Estimation of physical observables for unknown quantum states is an important problem that underlies a wide range of fields, including quantum information processing, quantum physics, and quantum chemistry. In the context of quantum computation, in particular, existing studies have mainly focused on holistic state tomography or estimation on specific observables with known classical descriptions, while this lacks the important class of problems where the estimation target itself relies on the measurement outcome. In this work, we propose an adaptive measurement optimization method that is useful for the quantum subspace methods, namely the variational simulation methods that utilize classical postprocessing on measurement outcomes. The proposed method first determines the measurement protocol for classically simulatable states, and then adaptively updates the protocol of quantum subspace expansion (QSE) according to the quantum measurement result. As a numerical demonstration, we have shown for excited-state simulation of molecules that (i) we are able to reduce the number of measurements by an order of magnitude by constructing an appropriate measurement strategy (ii) the adaptive iteration converges successfully even for a strongly correlated molecule of H4. Our work reveals that the potential of the QSE method can be empowered by elaborated measurement protocols, and opens a path to further pursue efficient quantum measurement techniques in practical computations.