Investigation of plasma-organic materials interaction in aqueous solution with atmospheric pressure plasmas have been carried out. Degradation of methylene blue (MB) in aqueous solution via atmospheric pressure He plasma exposure through gas/liquid interface have been investigated. The optical emission spectrum shows considerable emissions of He lines and the emission of O, OH and N radicals attributed to dissociation of water (H2O) and air has been confirmed. Structure variation of MB in solution treated with the atmospheric-pressure He plasma has been measured by Fourier transform infrared spectroscopy (FT-IR). The results obtained from FT-IR analysis show degradation of MB in solution treated with the atmospheric-pressure He plasma. The pH effect of MB degradation was investigated using controlled pH solutions by an ultraviolet-visible (UV-Vis) spectroscopy and FT-IR. The results show no effect of MB degradation on pH. The results exhibit that the atmospheric pressure plasmas exposure has made it possible to degrade organic materials in solution due to irradiated radicals from plasma through plasma/liquid interface.