High voltage light emitting diodes (HV-LEDs) have potential advantages on general lighting application for their special features. But as novel power LEDs, their optical, electrical and thermal characteristics still need to be further studied. In this paper, 6 and 9 V GaN-based HV-LEDs were packaged in the same package structure and process conditions. The optical characteristics of two samples were investigated under different temperatures range from 10 to 70 ℃ which were calibrated to junction temperatures using thermal impedance measurement. To ensure the same current density, working current was set to 150 mA for 6 V sample and 100 mA for 9 V sample respectively. Results show that the increasing junction temperature has a great effect on EL spectra of two samples, such as peak wavelength red-shifting, full width at half maximum (FWHM) broadening, luminous efficiency reducing and color rendering index (CRI) increasing. The junction temperature of 9V sample is lower than that of 6 V sample in the same platform temperature and injection power. With temperature increasing, the extended quantitative value of FWHM for 9 V sample is 1.3 nm less than that of 6 V sample, the reduced quantitative value of luminous efficiency is 1.13 lm·W-1 less than that of 6 V sample, while the increased quantitative value of CRI is 0.28 less than that of 6 V sample. Those data suggest that EL spectra of HV-LEDs is less affected by junction temperature than traditional LEDs. It is because HV-LEDs perform better in current spreading and generate less heat. This conclusion has reference value for study, development and applications of GaN-based HV-LEDs. In addition, peak wavelength still has a good linear relationship with junction temperature and it can be a temperature-sensitive parameter when the spectra measurement accuracy is enough.