We evaluate the baryon number abundance based on the charge transport scenario of top quarks in the CP-violating two Higgs doublet model, in which Yukawa interactions are aligned to avoid dangerous flavor changing neutral currents, and coupling constants of the lightest Higgs boson with the mass 125 GeV coincide with those in the standard model at tree level to satisfy the current LHC data. In this model, the severe constraint from the electric dipole moment of electrons, which are normally difficult to be satisfied, can be avoided by destructive interferences between CP-violating phases in Yukawa interactions and scalar couplings in the Higgs potential. Viable benchmark scenarios are proposed under the current available data and basic theoretical bounds. We find that the observed baryon number can be reproduced in this model, where masses of additional Higgs bosons are typically 300–400 GeV. Furthermore, it is found that the triple Higgs boson coupling is predicted to be 35–55 % larger than the standard model value.