Thermoelectric generators have been regarded as a prospective technique used for recovering engine exhaust heat. Segmented structure is more appropriate for large temperature gradient between the heat and cold source. This work establishes a numerical model of segmented thermoelectric generator for engine waste heat recovery based on the component level and system level simultaneously. Two patterns of p-n ratios are conducted to compare the properties between segmented and traditional models as well as optimize the segmented ratios under various conditions to get better performance. In the pattern of same p-n segmented ratios, the effects of structural parameters and thermodynamic boundary conditions on the output performance are analyzed. The optimal proportion of medium temperature material (CoSb3) increases with longer thermoelectric elements and higher heat transfer coefficient, whereas the cross section area shows hardly any influence on it. And then the power improvement capacity in view of the property difference between p-type and n-type material is investigated in the second pattern. The maximum output power is improved by approximately 13.8% compared with that of original segmented model. Finally, the application of optimal segmented ratio design in a thermoelectric generator system demonstrates better performance and further increases the output power by 6.8%.