INTRODUCTION: Autonomic dysfunction in patients with schizophrenia has raised concern considering the higher cardiovascular mortality and morbidity rate. This phenomenon has been demonstrated using various measurements and is inferred to be associated with demographics, medical treatment, and psychopathology. However, few have targeted the role of negative symptoms within schizophrenia. METHODS: Schizophrenia patients with stationary psychopathology were recruited from a chronic ward, a daycare center, and a nonintensive case management program. Demographic data, medication history, the Positive and Negative Syndrome Scale (PANSS) score, the Personal and Social Performance Scale (PSP) score, and the five-minute resting-state heart rate variability (HRV) were collected at trial initiation (Time 1) and a year later (Time 2). The relationships between variables and HRV indices were evaluated using correlation and regression analyses. RESULTS: A total of 63 participants were recruited at Time 1, with 29 participants remaining at Time 2. Correlation analyses showed a negative correlation between the PANSS negative score (PANSS-N) and total power (TP), low-frequency power (LF), and high-frequency power (HF) at Time 1. The results were further examined with multiple linear regression analysis and remained significant between the PANSS-N score and HF (beta = -0.306, P = .012). A generalized estimating equation model revealed the above negative association to be significant considering both timepoints. DISCUSSION: The negative association between negative symptom severity and parasympathetic activity was significant, which may inspire further research into the corresponding treatment, the mechanisms, and the use of HRV as an applicable biomarker for treatment response.