The study on photoelectronic characteristics of ZnSe quantum dots (QDs) is of significance for investigating its microelectronic structure and expanding its potential applications because ZnSe QD has low biologic toxicity. In the present paper, the surface photovoltaic and photoacoustic technologies, and laser Raman, X-ray diffraction, transmission electron microscopy and Foureier transform infrared spectroscopy spectrum are jointly used to probe the microstructures, the photoacoustic and surface photovoltaic characteristics of L-Cysteine-capped ZnSe QDs prepared by water-phase synthesis at different reflux temperatures. The results indicate that the ZnSe QDs with a mean grain size of about 3 nm has a core-shell ZnSe/ZnS/L-Cys structure, in which the sulfhydryl groups in ligand prefer reacting with Zn atom at the (220) face to form the ZnS shell layer between the core-ZnSe and ligand L-Cys. The results show that the QDs with n-type photovoltaic property display a wide range of surface photovoltaic response and weak photoacoustic signal upon the illumination of near ultraviolet to visible light as compared with others QDs with similar core-shell structures in II-VI group. Especially, the strong SPV response and the weak PA signal in a wavelength region of 350-550 nm imply that the photon energies in the range are almost all used to produce the surface photovoltaic (SPV) phenomenon instead of the thermal lattice vibration caused by non-radiative de-excitation process. This reveals the energy complementary relationship between the photoacoustic and the surface photovoltaic phenomena of the QDs. The PA signals appearing in a short wavelength range of 300-350 nm and the Raman peaks located in a high frequency ranges of 1120 cm-1, 1340 cm-1 and 1455 cm-1 are identified as relating closely to the multi-phonon vibration modes of ligand L-Cys. At low reflux temperature, the photoelectric threshold of the SPV response that relates to the core-ZnSe displays a red shift to a certain extent as compared with the bulk ZnSe. The narrowed bandgap may be attributed to quantum confinement effect of the QDs. In addition, the intensity of the SPV response that relates to the core-ZnSe gradually increases with the decrease of the reflux temperature. The results show that the above improved surface photovoltaic characteristics of the QDs may benefit from the reduced average grain size of the ZnSe QDs, thus causing its surface and small-size effects.