The structural and vibrational properties of ZnnSen (n=1,3,7,13) nanostructures have been investigated using the Gaussian 09 program, density functional theory and time-dependent density functional theory at the B3LYP level with 6–311G basis functions. The structural properties showed that the rebuilding in surface atoms deviated many bonds from their ideal length, the Zn-Se bond length decreased with the increase in the size of nanostructures and converged to the experimental value. Quantum confinement effect diminution was observed with the growing size of the nanostructures; hence, the energy gap converged to the experimental value of 2.7 eV. Moreover, the binding energy increased with the increase of the structure size, such that wurtziod2c (Zn13Se13) is more stable than smaller structures. The vibrational properties results indicated that the experimental longitudinal optical mode (LO mode) is situated between bare and hydrogen passivated LO modes and very near to the bare case, this gave a good agreement with experimental findings. The presence of hydrogen atoms at the surface caused a several times decrease in vibrational force constant in comparison to the bare case. The IR spectrum for wurtzoid and HP wurtzoid were investigated. The optical edge in UV-Vis spectra of wurtzoid reduced from 4.5 eV to 4.2 eV of wurtzoid2c due to the increase in the size of the nanostructure, while the maximum peak for wurtzoid at 2.88 eV increased to 3.06 eV for wurtzoid2c showing a clear blue shift. These results leads to wide applications in fields such as photoelectronic devices, lasers, sensors, and LEDs.