The theory of structural dissociation of the personality proposes that patients with complex trauma-related disorders are characterized by a division of their personality into different prototypical parts, each with its own psychobiological underpinnings. As one or more apparently normal parts (ANPs), patients have a propensity toward engaging in evolutionary prepared action systems for adaptation to daily living to guide their actions. Two or more emotional parts (EPs) are fixated in traumatic experience. As EPs, patients predominantly engage action systems related to physical defense and attachment cry. ANP and EP are insufficiently integrated, but interact and share a number of dispositions of the personality (e.g., speaking). All parts are stuck in maladaptive action tendencies that maintain dissociation, including a range of phobias, which is a major focus of this article. Phase-oriented treatment helps patients gradually develop adaptive mental and behavioral actions, thus overcoming their phobias and structural dissociation. Phase 1, symptom reduction and stabilization, is geared toward overcoming phobias of mental contents, dissociative parts, and attachment and attachment loss with the therapist. Phase 2, treatment of traumatic memories, is directed toward overcoming the phobia of traumatic memories, and phobias related to insecure attachment to the perpetrator(s), particularly in EPs. In Phase 3, integration and rehabilitation, treatment is focused on overcoming phobias of normal life, healthy risk-taking and change, and intimacy. To the degree that the theory of structural dissociation serves as an integrative heuristic for treatment, it should be compatible with other theories that guide effective treatment of patients with complex dissociative disorders.