In this paper, ZnO nano-particles (NPs) were modified by adding a dispersant (n-propylamine, PA) and a silane coupling agent (1H, 2H, 1H, 2H, Perfluorooctyltriethylsilane, PFOES) simultaneously. Further, the PVDF-TrFE/modified ZnO composite films with high crystallinity and large specific surface area were prepared, which acted as the active layer of the piezoelectric nanogenerator (PENG). Four species of films, pure PVDF-TrFE, PVDF-TrFE/ZnO, PVDF-TrFE/ZnO@PA and PVDF-TrFE/ZnO@PA@PFOES were marked P-0-0-0, P-Z-0-0, P-Z-P-0 and P-Z-P-P, respectively. The crystalline phases of the films were determined by Fourier infrared spectroscopy (FTIR) and wide-angle X-ray diffraction (WXRD). Scanning electron microscope (SEM), Laser scanning confocal microscope (LSCM), Atomic force microscope (AFM) and water contact angle (WCA) measurements were employed to analyze the surface morphology of the films. The thermal properties of the materials were characterized with a differential scanning calorimeter (DSC). From the FTIR spectra and WXRD pattern, it was notable that the modified ZnO NPs promoted the crystallization of beta-phase. The results showed that the crystallinity of P-Z-P-P was increased by 36.12% compared to P-0-0-0. Combined with the results of SEM, LSCM and AFM, it can be concluded from WCA that modified ZnO NPs can increase the specific surface area of the film. The piezoelectric strain constant d(33) value of P-Z-P-P film was 73.5% higher than that of P-0-0-0 film, and the output voltage value of ITO/P-Z-P-P/Au PENG increased 24.4% than that of ITO/P-0-0-0/Au PENG. After 1000 cycles of testing, the output voltage of the ITO/P-Z-P-P/Au PENG has been maintained at 2.40 V, indicating that the generator exhibited the high mechanical endurance. By clarifying the mechanism of surface modification, it can be concluded that enhanced piezoelectric output of the PENG is contributed to both higher beta-phase content and larger charge collecting area by surface modification.