The Jiangmen Underground Neutrino Observatory (JUNO) is proposed as a multipurpose neutrino experiment , whose primary goal is to determine the neutrino mass ordering (NMO) and precisely the neutrino oscillation parameters via reactor neutrino at 3-4 σ within 6 years. The neutral-current (NC) of atmospheric neutrino interactions with the C12 nuclei in the liquid scintillator (LS) would constitute an important background in the low energy range from reactor neutrinos to the diffuse supernova neutrino background (DSNB).In this poster, we make a systematic study on the atmospheric NC background. Different neutrino generators (GENIE, GiBUU and NuWro) are used for simulating the neutrino interactions with the carbon nuclei in LS, and the de-excitations of final state nuclei are treated with TALYS. The characteristics of the NC interactions under different models are compared to evaluate the associated uncertainty. Finally, the prediction of the NC background is presented based on different generators after the detector simulation. This new understanding would help to better understand the impact of the NC background, and important for JUNO to achieve its physics goal in NMO and DSNB research.