Abstract Flexible p–n thermoelectric generator (TEG) technology has rapidly advanced with power enhancement and size reduction. To achieve a stable power supply and highly efficient energy conversion, absolute chemical stability of n‐type materials is essential to ensuring large temperature differences between device terminals and ambient stability. With the aim of improving the long‐term stability of the n‐type operation of carbon nanotubes (CNTs) in air and water, this study uses cationic surfactants, such as octylene‐1,8‐bis(dimethyldodecylammonium bromide) (12–8–12), a gemini surfactant, to stabilize the nanotubes in a coating, which retains the n‐doped state for more than 28 days after exposure to air and water in experiments. TEGs with 10 p–n units of 12–8–12/CNT (n‐type) and sodium dodecylbenzene sulfonate/CNT (p‐type) layers are manufactured, and their water stability is evaluated. The initial maximum output of 16.1 µW (75 K temperature difference) is retained after water immersion for 40 days without using a sealant to prevent TEG module degradation. The excellent stability of these CNT‐based TEGs makes them suitable for underwater applications, such as battery‐free health monitoring and information gathering systems, and facilitates the development of soft electronics.