The function of SCR system in refuse incineration plant is to reduce the harmful combustion gases especially NOx which make serious environmental pollution. The SCR system normally have a NOx measurement system such as inlet NOx analyzer and outlet T.M.S.(Tele Monitoring System) to control the outlet NOx in stack. The NOx measurement system is very important, however there are frequently happened sensing problems and it need maintenance periodically. In this paper, we propose an estimation method of inlet NOx of SCR system by using general structured observer. The inlet NOx is considered as an input disturbance and it is modelled by applying FFT method in frequency domains. Through the design of general structured observer, the outlet NOx can be estimated by using observation error between real outlet NOx and estimated outlet NOx. The effectiveness of the proposed method is shown by comparing to a measured inlet NOx data.