A thermoelectric generator (TEG) is one of the important energy harvesting sources for wearable electronic devices, which converts waste heat into electrical energy without any external stimuli, such as light or mechanical motion. However, the poor flexibility of traditional TEGs (e.g., Si-based TE devices) causes the limitations in practical applications. Flexible paper substrates are becoming increasingly attractive in wearable electronic technology owing to their usability, environmental friendliness (disposable, biodegradable, and renewable materials), and foldability. The high water-absorbing quality of paper restricts its scope of application due to water failure. Therefore, we propose a high-performance flexible waterproof paper-based thermoelectric generator (WPTEG). A modification method that infiltrates TE materials into cellulose paper through vacuum filtration is used to prepare the TE modules. By connecting the TE-modified paper with Al tape, as well as a superhydrophobic layer encapsulation, the WPTEG is fabricated. The WPTEG with three P–N modules can generate an output voltage of up to 235 mV at a temperature difference of 50 K, which can provide power to portable electronic devices such as diodes, clocks, and calculators in hot water. With the waterproof property, the WPTEG paves the way for achieving multi-scenario applications in humid environments on human skin.