We give a perturbation theory of neutrino oscillation in the Earth. The perturbation theory is valid for neutrinos with energy $E \gsim 0.5$ GeV. It is formulated using trajectory dependent average potential. Non-adiabatic contributions are included as the first order effects in the perturbation theory. We analyze neutrino oscillation with standard matter effect and with non-standard matter effect. In a three flavor analysis we show that the perturbation theory gives a precise description of neutrino conversion in the Earth. Effect of the Earth matter is substantially simplified in this formulation.