This paper investigated the combustion instability of spanwise positions in a hydrogen fueled scramjet combustor with a cavity flame holder. High-speed OH-PLIF technique was performed on a direct-connect supersonic combustion facility, and dynamic mode decomposition (DMD) as postprocessing. Combustion instability was investigated by characterizing the dominant frequencies and growth factors. By changing the equivalence ratio of hydrogen, the peak frequencies of scramjet mode and ramjet mode were obtained. Scramjet mode tended to have small oscillation at 150-200 Hz reflected by negative growth factors due to the stable flame structure. At ram-to-scram transition, oscillations at 80-120 Hz were remarkably enhanced due to the positive growth factors. In ramjet mode, the large differences of frequency characteristics in spanwise positions were observed. The dominant DMD modes near the cavity wall appeared to have negative growth factors leading to a stable flame with small oscillations. Besides, the characteristics of frequency-shift were affected by the positions of injector. (C) 2020 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.