As Bojidarka said: the system size will determine the level of theory and basis set size you can use. B3LYP/6-31+g(d,p) is a good starting point but you can check what effect changing the basis set has on your results (try the DEF2QZVP basis set for instance). For small systems you might be able to use MP2 or B2PLYPD3 methods for comparison.
Thank you all for your valuable suggestions. Finally, I got the idea and used the MO6-2X functional with the Aug-cc-pVTZ because my molecule was having a negative charge and this functional is the best for calculating thermochemistry especially BDE.