A triboelectric nanogenerator (TENG) can convert mechanical energy from its surroundings into electricity. Surface properties such as surface area and surface potential are important variables for improving triboelectric performance. Thus, surface engineering is a promising technique for enhancing triboelectric performance. In this work, for the first time, we introduce a neutral beam based surface modification for enhancing triboelectric performance. First, we investigate appropriate NB treatment conditions for polydimethylsiloxane (PDMS) and thermoplastic polyurethane (TPU) that are used as the negative and positive triboelectric material, respectively. Secondly, we defined the optimal pairing of NB-treated PDMS and TPU for maximizing output performance. Then, we demonstrated the surface stability of NB-treated TENGs by comparing electrical output performances with plasma-treated TENGs for 3 months. Throughout this work, we showed the effect of NB treatments on the triboelectric performance of the TENG device. We expect that our results can provide a new method for improving performance of TENGs for self-powered systems.