Abstract We present multi-wavelength studies of optically defined merging clusters, based on the Hyper Suprime-Cam Subaru Strategic Program. Luminous red galaxies, tracing cluster mass distributions, enable us to identify cluster subhalos at various merging stages, and thus make a homogeneous sample of cluster mergers that is unbiased with respect to the merger boost of the intracluster medium (ICM). We define, using a peak-finding method, merging clusters with multiple peaks and single clusters with single peaks from the CAMIRA cluster catalog. Stacked weak-lensing analysis indicates that our sample of merging clusters is categorized into major mergers. The average halo concentration for the merging clusters is ∼70% smaller than that of the single-peak clusters, which agrees well with predictions of numerical simulations. The spatial distribution of subhalos is less centrally concentrated than the mass distribution of the main halo. The fractions of red galaxies in the merging clusters are not higher than those of the single-peak clusters. We find a signature of the merger boost of the ICM from the stacked Planck Sunyaev–Zel’dovich effect and ROSAT X-ray luminosity, but not in optical richness. The stacked X-ray surface brightness distribution, aligned with the main subhalo pairs of low-redshift and massive clusters, shows that the central gas core is elongated along the merger axis, and overall gas distribution is misaligned by ∼60°. The homogeneous, unbiased sample of cluster mergers and multi-wavelength follow-up studies provide a unique opportunity to make a complete picture of merger physics over the whole process.