Abstract: Recently, atom-based microwave (MW) measurement has inspired great interest because of its potential ability to link the MW quantity with the international system of units (SI) second. The frequency has the highest measurement accuracy among all physical quantities, implying a great potential of atomic MW measurement. At present, the main factor limiting the measurement accuracy arises from atomic vapor-cell itself. In order to evaluate the effects of the vapor-cell on atom-based MW measurements, the structure parameters and permittivity of vapor-cell are firstly estimated in this paper. As a demonstration, the complex permittivity of a cylindrical vapor-cell is measured and evaluated through MW cavity perturbation technique at S and X bands. Finally, various methods used for the measurement of permittivity of vapor-cell are briefly discussed.