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This paper introduces the concept of auto–Engel polygroups via the heart of hypergroups and investigates the relation between of auto–Engel polygroups and auto–nilpotent polygroups. Indeed, we show that the concept of heart of hypergroups plays an important role on construction of auto–Engel polygroups. This study considers the notation of characteristic set in hypergroups with respect to automorphism of hypergroups and shows that the heart of hypergroups is a characteristic set in hypergroups.