This study aims to analyze the relationship between the sociocognitive skills of a group of children and adolescents with autism spectrum disorder (ASD) at verbal level 1, the variability of the therapist’s heart rate (HRV), and the conversational turn-taking during online psychotherapy sessions. Initially, we assessed the intelligence, narrative, and behavioral characteristics of the participants. We videotaped the online sessions and recorded the therapist’s HRV via a smart wireless sensor. Finally, we analyzed the video sessions using an observation system and the therapist’s HRV using the Poincaré technique. The results show that the patients’ communicative intention was related to their narrative, intellectual and social competencies. Furthermore, the turn-taking between the therapist and the participant was associated with the patient’s emotional and behavioral difficulties. On the other side, the therapist’s heart rate variability (HRV) was related to the synchrony between the therapist and the participant with more significant stress on the therapist, when he shared and expanded the conversation with the patient, and when the patient broadened and shared the conversation with the therapist.