We perform weak lensing tomographic peak studies using the first-year shear data from Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP) survey. The effective area used in our analyses after field selection, mask and boundary exclusions is $\sim 58 \deg ^2$. The source galaxies are divided into low- and high-redshift bins with 0.2 ≤ zp ≤ 0.85 and 0.85 ≤ zp ≤ 1.5, respectively. We utilize our halo-based theoretical peak model including the projection effect of large-scale structures to derive cosmological constraints from the observed tomographic high peak abundances with the signal-to-noise ratio in the range of νN = [3.5, 5.5]. These high peaks are closely associated with the lensing effects of massive clusters of galaxies. Thus the inclusion of their member galaxies in the shear catalog can lead to significant source clustering and dilute their lensing signals. We account for this systematic effect in our theoretical modelling. Additionally, the impacts of baryonic effects, galaxy intrinsic alignments, as well as residual uncertainties in shear and photometric redshift calibrations are also analyzed. Within the flat ΛCDM model, the derived constraint is $S_8=\sigma _8(\Omega _{\rm m}/0.3)^{0.5} =0.758_{-0.076}^{+0.033}$ and $0.768_{-0.057}^{+0.030}$ with the source clustering information measured from the two cluster catalogs, CAMIRA and WZL, respectively. The asymmetric uncertainties are due to the different degeneracy direction of (Ωm, σ8) from high peak abundances comparing to that from the cosmic shear two-point correlations which give rise approximately the power index α = 0.5. Fitting to our constraints, we obtain α ≈ 0.38 and $\Sigma _8=\sigma _8(\Omega _{\rm m}/0.3)^{\alpha }=0.772_{-0.032}^{+0.028}$ (CAMIRA) and $0.781_{-0.033}^{+0.028}$ (WZL). In comparison with the results from non-tomographic peak analyses, the 1σ uncertainties on Σ8 are reduced by a factor of ∼1.3.