Poor light extraction efficiency (LEE) has been one of the major challenges responsible for the low external quantum efficiency of AlGaN-based ultraviolet light emitting Diodes (UV-LEDs). In this study, AlGaN nanostructure arrays were fabricated using a large-scale nanosphere self-assembly technique followed by reactive ion etching, and the transmission property of the AlGaN thin film and the photoluminescence (PL) behavior of AlGaN/GaN multiple-quantum-wells (MQWs) were investigated. A 90% light transmission value was obtained for the AlGaN thin film and a 2.5-fold increase in the band edge luminescence of the MQWs were obtained with an optimized nanostructure periodicity. Essentially, a general rule of periodicity-MQW emission wavelength matching criteria-was provided. Both the light transmission properties of the Al_0.55Ga_0.45N/AlN/sapphire thin film and the photoluminescence (PL) behavior of the AlGaN/GaN MQWs contribute to an improved understanding of the light extraction mechanism of PhC patterned UV-LEDs. Raman spectra also demonstrated the strain relaxation inside the MQW after nanostructure fabrication and thermal annealing. This study provides a pathway towards higher efficiency UV-LEDs with the help of a periodicity-wavelength matched nanostructure array.