A new method for determining the average junction temperature of AlGaInP-based light emitting diode (LED) array is developed based on the difference of normalized spectral distribution. The normalized spectra of three LED arrays with various injected powers and substrate temperatures are measured with a spectrometer, and the relationship between the differences of normalized spectral distributions and the average junction temperatures of LED arrays is analyzed. The accuracy of evaluating junction temperature with the difference of normalized spectral distributions is compared with the proposed method using center wavelength shift. The results show that the difference of normalized spectral distributions, measured with a spectrometer of 1 nm sample interval, changes linearly with the variation of average junction temperature whether it is induced by the change of the injected power or the substrate temperature, and the linearity is better than that of the method using center wavelength shift. Therefore, the difference of normalized spectral distributions can be used to estimate the average junction temperature, and the accuracy is better than the method using center wavelength shift.