Previous studies have proposed a connection between dissociation and the sense of body ownership, and initial evidence suggests that emotions could modulate this relationship. Here we aimed to investigate how differently arousing emotions influence the malleability of the bodily self. This study included 50 adolescent psychiatric patients with non-suicidal self-injurious behavior (NSSI)—who were divided into low-dissociation and high-dissociation groups—along with 25 healthy controls. Participants completed six trials of the rubber hand illusion while listening to neutral, sad, or fearful vocalizations. Heart rate, skin conductance level, and non-specific skin conductance responses were concomitantly measured. After each trial, participants completed the rubber hand illusion questionnaire as a subjective illusion measure, and acute dissociation, mood, and proprioceptive drift were assessed. Overall, the NSSI high-dissociation group reported the highest subjective illusion under all conditions. Additionally, fearful vocalizations resulted in a stronger subjective illusion than the neutral condition in the NSSI low-dissociation group, but not in the NSSI high-dissociation and healthy control groups. The NSSI low-dissociation group showed a higher proprioceptive drift than the NSSI high-dissociation group. Moreover, acute dissociation was positively related to subjective illusion, but not related to proprioceptive drift. In conclusion, body detachment in response to emotions may be responsible for the malleability of the sense of body ownership. This finding highlights the need for clinical interventions to stabilize self-experiences during emotional situations, especially in patients with dissociative symptoms.