The introduction of functional groups at high coverage levels can have significant impacts on the band structures of polycyclic aromatic hydrocarbon (PAH) clusters. The HOMO-LUMO gaps are highly sensitive to the type and distribution of functional groups. An in-house method is proposed to build PAH (naphthalene, pyrene, coronene, and ovalene) clusters with surface functionalization of -OH, -COOH and -CHO groups using the DFT method. The -CHO groups are found to reduce the gap value the most, but exceptions exist due to the spatial distribution of functional groups. Considering the impact of -CHO groups only, we can approximate that the impact of functional groups lies in the range of 0.14-0.89 eV. Applying further analysis on the possible energy number of energy transitions of substituted PAH clusters, it is shown that PAH clusters with oxygenated functions still behave like an indirect band gap material. The coupling effect of PAH stacking and PAH size is also addressed. A simple expression is proposed to estimate the bandgap of a mixed system using the HOMO and LUMO energy of the two components. Further attempts are made to interpret recent experiments from the impact of PAH stacking, PAH size, and functional groups.