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Abstract In the development of high‐performance organic thermoelectric devices, n‐type materials, especially with small molecule semiconductors, lags far behind p‐type materials. In this paper, three small molecules are synthesized based on electron‐deficient naphthalene bis‐isatin building blocks bearing different alkyl chains with the terminal functionalized with 3‐ethylrhodanine unit and studied their aggregation and doping mechanism in detail. It is found that crystallinity plays an essential role in tuning the doping behavior of small molecules. Molecules with too strong crystallinity tend to aggregate with each other to form large crystalline domains, which cause significant performance degradation. While molecules with weak crystallinity can tolerate more dopants, most of them exhibit low mobility. By tuning the crystallinity carefully, organic thermoelectric devices based on C12NR can maintain high mobility and realize effective doping simultaneously, and a high power factor of 1.07 µW m−1 K−2 at 100 °C is realized. This delicate molecular design by modulating crystallinity provides a new avenue for realizing high‐performance organic thermoelectric devices.