Third-order nonlinear optical analysis of aryl-substituted 4, 4-difluoro-4-bora-3a, 4a-diaza-s-indacene (BODIPY) derivatives and their hybrid system with ZnSe nano structures, by Z-scan technique under ns pulse excitation is reported. A red shift was observed in the linear absorption spectra of the hybrid system compared to their counter parts. The hybrid system formation was also verified with the help of FTIR spectra and morphological changes were revealed from SEM images. Saturable absorption assisted excited state absorption was found to be the mechanism behind the optical nonlinearity of BODIPYs and the brominated derivatives showed a switching behaviour from saturable absorption to reverse saturable absorption on increasing the input intensity. The mentioned switching behaviour and optical nonlinearity of BODIPYs were found to be modified on incorporating with ZnSe nanostructures. All the samples exhibited negative optical nonlinearity which was revealed under closed aperture Z-scan studies and hybrid system formation assured the enhancement in the coefficients of nonlinear refractive index. The charge/energy transfer between the constituents of the hybrid system could be accredited to the improved nonlinear optical properties of the system.