In this work, three GaN-based multiple quantum well (MQW) samples are grown to investigate the growth techniques of high-quality MQWs at low temperature (750 °C). Instead of conventional temperature ramp-up process, H2/NH3 gas mixture was introduced during the interruption after the growth of InGaN well layers. The influence of hydrogen flux was investigated. The cross-sectional images of MQW via transmission electron microscope show that a significant atomic rearrangement process happens during the hydrogen treatment. Both sharp interfaces of MQW and homogeneous indium distribution are achieved when a proper proportion of hydrogen was used. Moreover, the luminescence efficiency is improved strongly due to suppressed non-radiative recombination process and a better homogeneity of MQWs. Such kind of atomic rearrangement process is mainly caused by the larger diffusion rate of gallium and indium adatoms in H2/NH3 mixed gas, which leads to a lower potential barrier energy to achieve thermodynamic steady state. However, when excessive hydrogen flux is introduced, the MQW will be partly damaged, and the luminescence performance will deteriorate.