Band alignment is key to enhance the performance of heterojunction for chalcopyrite thin film solar cells. In this paper we report ab initio calculations of the electronic structures of CuGaS2:Cr with various Cr compositions, CuAlSe2 and ZnSe and the band alignment between their interfaces. We use density functional theory and the more accurate self-consistent GW scheme to obtain improved bulk band-gaps and band offsets. Band alignments of the interfacial region for CuGaS2:Cr/CuAlSe2 and CuGaS2:Cr/ZnSe systems were aligned with respect of an average electrostatic potential. Our results are in good agreement with experimental values for the bulk band-gaps. These theoretical band alignments show a characteristic staggered band alignment for the design of heterojunction devices in photovoltaic applications.