Future large liquid-scintillator (LS) detectors are competitive with and complementary to the water-Cherenkov detectors on the searches for diffuse supernova neutrino background and nucleon decay. In a companion paper, we have performed a systematic calculation of the neutral-current (NC) background induced by atmospheric neutrino interactions on nuclei in LS detectors, which are expected to be crucially important for the experimental searches for the diffuse supernova neutrino background and nucleon decay. In this paper, we perform a systematic study on the measurement of the NC background and evaluate the associated uncertainties. We first exploit the characteristics of the NC background, in particular, the multiplicities of neutrons and pions, and the possible association with unstable residual nuclei. It turns out that the neutron multiplicity distribution is very powerful to discriminate among different models. Then, we develop a maximum-likelihood method to allow an in situ measurement of the NC interactions with a triple-coincidence signature. Finally, a data-driven approach is proposed to evaluate the uncertainty of the NC background in the search for the diffuse supernova neutrino background. We conclude that future large LS experiments like the Jiangmen Underground Neutrino Observatory will be able to make a unique contribution to the worldwide dataset to improve the prediction of atmospheric neutrino NC interactions on .