Thermoelectric (TE) charge transport in organic TE nanocomposite systems is a critical consideration in designing high-performance TE materials. Here, the relationship between the TE properties and energy structure of conducting polymer/quantum dot (QD) nanocomposites is systematically investigated by developing a potential wall or potential well in poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) with CdTe QDs. The added QDs are primarily distributed within the electrically insulating PSS shell and act as stepping stones for charge transport between PEDOT-rich grains. The embedded QDs generate an energy-filtering effect, which is induced by both potential wall and potential well states established by the QDs in the PEDOT:PSS films. The induced energy-filtering effect increases the Seebeck coefficient S with limited loss of electrical conductivity σ, thereby overcoming the TE trade-off relation S ∝ σ