Intrinsic atomic defects pose a great effect in wide-bandgap semiconductors owing to the high tendency of forming in-gap defective states. Utilizing density-functional theory, the atomic vacancy defects of Al and N vacancies in hexagonal wurtzite aluminum nitride (AlN) are investigated. We find that the most energetically favorable form of vacancies is predicted to be negatively trivalent charged Al vacancy (V) in n-type AlN and positively monovalent charged N vacancy (V) in p-type AlN, respectively. N vacancy generally has a low formation energy and could be either an acceptor or a donor: Under p-type conduction, it is a deep donor with a positively monovalent charge of +1, acting as a compensating center for holes; Under n-type conduction, it is a deep acceptor carrying charge of −3, acting as a compensating center for electrons. For the Al vacancy, it tends to be a shallow acceptor in p-type AlN but a high formation energy or a deep acceptor in n-type AlN with low formation energy, most possibly at a negatively trivalent charged state. Our orbital hybridization analysis shows that these vacancies can be facilely generated which are rooted in the antibonding coupling Al-N states in valence band. The above finding is independent of the chemical potential of nitrogen and aluminum and holds true under both nitrogen rich and poor conditions. Our work provides a guide to experimental works by providing the energetics and atomic-scale mechanism of doping nature of atomic vacancies in AlN.