Abstract The formation mechanism of high-concentration dwarf galaxies is still a mystery. We perform a comparative study of the intrinsic shape of nearby low-mass galaxies with different stellar concentration. The intrinsic shape is parameterized by the intermediate-to-major axis ratios B/A and the minor-to-major axis ratios C/A of triaxial ellipsoidal models. Our galaxies (107.5 M ⊙ < M ⋆ < 1010.0 M ⊙) are selected to have spectroscopic redshift from SDSS or GAMA and have broadband optical images from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP) wide-layer survey. The deep HSC-SSP images allow to measure the apparent axis ratios q at galactic radii beyond the central star-forming area of our galaxies. We infer the intrinsic axis ratios based on the q distributions. We find that (1) our galaxies have typical intrinsic shape similarly close to be oblate (μ B/A ∼ 0.9–1), regardless of the concentration, stellar mass, star formation activity, and local environment (being central or satellite); (2) galaxies with the highest concentration tend to have intrinsic thickness similar to or (in virtually all cases) slightly thinner (i.e., smaller mean μ C/A or equivalently lower triaxiality) than ordinary galaxies, regardless of other properties explored here. This appears to be in contrast with the expectation of the classic merger scenario for high-concentration galaxies. Given the lack of a complete understanding of dwarf–dwarf merger, we cannot draw a definite conclusion about the relevance of mergers in the formation of high-concentration dwarfs. Other mechanisms such as halo spin may also play important roles in the formation of high-concentration dwarf galaxies.