Tussah pebrine disease resulting from Nosema bombycis (NB) spores causes massive production and economic losses in the silk industry in China. This paper reports on highly effective inactivation of NB spores for the control of pebrine disease by using an atmospheric pressure cold plasma jet. Both Giemsa dyeing measurement and tussah breeding experiment show that the atmospheric pressure He plasma jet containing 1% kills almost all the NB spores with a population within an exposure time of 5 min. Scanning electron microscopy measurements and UV absorbance spectra show that plasma inactivation has withered up the NB spores and resulted in the spores inactivated. Both energy dispersive spectroscopy and optical emission spectroscopy measurements showed that plasma-created reactive particles, such as O and accompanied charged species can play an important role in the inactivation processing.