We study electroweak baryogenesis driven by the top quark in two Higgs doublet model that allows flavor-changing neutral Higgs couplings. Taking Higgs sector couplings and the additional top Yukawa coupling $\rho_{tt}$ to be $\mathcal{O}$(1), one naturally has first order electroweak phase transition and sufficient $CP$ violation to fuel the cosmic baryon asymmetry. Even if $\rho_{tt}$ vanishes, the favor-changing coupling $\rho_{tc}$ can still achieve baryogenesis. Phenomenological consequences such as $t\to ch$, $\tau \to \mu\gamma$, electron electric dipole moment, $h\to\gamma\gamma$, and $hhh$ coupling are discussed. The extra scalars $H^0$, $A^0$ and $H^\pm$ are sub-TeV in mass, and can be searched for at the LHC.