Heterojunction GaN/MoSe2 has recently piqued the interest of researchers due to its exceptional electronic and optical properties. Despite this, the higher rate of photogenerated carrier recombination limits their technical application. Implementing a promising approach to the formation of the 2D heterostructure with vacancies may improve photocatalytic activity. By first-principles, the stability, electronic structure, and optical properties of monolayer GaN and MoSe2, GaN/MoSe2 (GN/MS), GaN/MoSe2 with a Ga vacancy (VGa-GN/MS), GaN/MoSe2 with an N vacancy (VN-GN/MS), and GaN/MoSe2 with vacancies of Ga and N (VGa@N-GN/MS) are systematically computed. Compared with monolayer GaN, MoSe2, and GaN/MoSe2, the results show that vacancies do not destroy the stability of heterojunctions and cause a decrease in their bandgaps and a redshift of the absorption spectra. Type-II band alignment is observed through Perdew–Burke–Ernzerhof calculations in all heterostructures. VGa-GN/MS and VGa@N-GN/MS are p-type semiconductors, while VN-GN/MS is an n-type semiconductor. Based on the analysis of Mulliken occupancy, work function, and optical properties, we speculate that vacancies of Ga and N cause GN/MS to be energetically favorable for water splitting.