Self interacting massive particles created as a consequence of thermal production in the early Universe are one of the most theoretically motivated candidate of dark matter (DM). Those particles can emit gamma rays through annihilation processes and contribute to an observed cosmic gamma-ray flux, and thus measurements of extragalactic gamma-ray allow us to probe the nature of DM. In particular, annihilation cross-sections for DM has been constrained by comparing the observed gamma-ray flux with a model of gamma-ray flux induced by DM annihilation within nearby objects like Milky Way dwarf spheroidals (dSphs). In this work, we propose that low surface brightness galaxies (LSBGs) can be used as novel tracers of DM annihilation signals because those galaxies are more massive than Milky Way dSphs, which leads to production of more luminous gamma-ray flux by DM annihilation. Moreover, it is expected to be less contaminated by extragalactic gamma-ray sources (e.g., blazars) compared to star forming galaxies. We find that the upper limit with a joint analysis of the eight LSBGs detected by Subaru Hyper Suprime-Cam survey data and exclude (at the 95% confidence level) the annihilation cross-section for the b_b channel higher than ~10^{-23} [cm^3/s] for DM mass of 10 GeV. However our constraint is weaker than the ones reported in recent studies using other targets, we note that in near future observations, the number of LSBGs should be a few orders of magnitude larger, and the constraint with LSBGs on the DM annihilation cross-section can become stronger than the ones from other probes.