Manipulation of the surface properties of the triboelectric layer has been proven to be one of the key parameters to achieve high-performance and stable triboelectric nanogenerators (TENG). Herein, a pragmatic surface engineering strategy that can substantially boost the performance and stability of flexible TENG is elaborated by incorporating the zwitterionic molecule dimethylethylammoniumpropane sulfonate (NDSB) as the surface modification layer. Given that zwitterionic molecules tend to form aggregated structures, realizing ordered arrangement on the substrate surface remains challenging to date. To address this issue, in this work, a combination of multiple surface treatments and molecular manipulation strategy is proposed. Our results prove that NDSB is effective in modifying the surface properties of the dielectric layer and electrode layer, leading to a remarkable power density and specific power of 2.86 W m⁻² and 20.73 mW g⁻¹ for flexible TENG, respectively. In addition, due to the strong interaction between the NDSB/dielectric and NDSB/electrode, a water-resistant long-term stable flexible TENG is realized. More encouragingly, our strategy is compatible with a cost-effective dip-coating technique, and an unprecedented demonstration of batch fabrication of TENG using NDSB to functionalize the surface of the dielectric layer and electrode layer synchronously can be realized, which is advantageous for rapid and up-scalable manufacturing of TENG. We also prove that the TENG based on zwitterionic materials reveals exceptional antibacterial properties against Escherichia coli. This study represents an important step towards the development of long-term stable flexible TENG that possesses a high output performance and excellent antibacterial activity based on a facile and economical strategy, enabling TENG technology to show bright prospects in a wide variety of application domains.