The use of organic–inorganic nanocomposites has shown the greatest potential for engineering efficient flexible thermoelectric devices. In this work, a novel approach of encapsulation of as‐grown bismuth selenide‐multiwalled carbon nanotubes (Bi2Se3‐MWCNT) hybrid network in polyvinyl alcohol for fabrication of n‐type flexible thermoelectric films is demonstrated as a successful alternative to the mechanically mixed counterparts. The developed stable flexible n‐type thermoelectric material has a Seebeck coefficient and power factor at room temperature as high as −85 μV K−1 and 0.4 μW m−1 K−2, and figure‐of‐merit, exceeding the value shown by the mixed counterpart by ≈2 orders of magnitude, while requiring 3–4 times less inorganic material in comparison with mixed composites. Charge carrier transport mechanisms and contribution of Bi2Se3 and MWCNT components of not encapsulated and encapsulated hybrid networks to the total Seebeck coefficient, electrical conductance, and power factor are studied. In addition, the fabricated flexible thermoelectric films show good environmental stability at relative humidity levels up to 60%, as well as great mechanical and electrical stability with the increase of resistance within 0.5% and deviations of the Seebeck coefficient within 2% from the initial value during the 100 repetitive bending cycles. A novel technique for fabrication of flexible n‐type thermoelectric nanocomposites by encapsulating as‐grown Bi2Se3‐ multiwalled carbon nanotube hybrid networks in nonconductive poly(vinyl alcohol) without disruption of the interconnects formed in the hybrid network during its growth is demonstrated. This innovative and simple method results in obtaining flexible and highly durable thermoelectric films with two times higher figure of merit in comparison with the state‐of‐the‐art counterparts.