Background: Work stress is considered as a risk factor for coronary heart disease, but its link with heart rate variability (HRV) among heart attack survivors is unknown yet. The aim of this study was to investigate associations between baseline work stress and the changes of HRV over one-year after onset of acute coronary syndrome (ACS). Methods: Hundred and twenty-two patients with regular paid work before their first ACS episode were recruited into this hospital-based longitudinal cohort study. During hospitalization (baseline), all patients underwent assessments of work stress by job strain (JS) and effort-reward imbalance (ERI) models, and were assigned into low or high groups; simultaneously, sociodemographic and clinical data, as well depression, anxiety, and job burnout, were collected. Patients were followed up 1, 6, and 12 months after discharge, with HRV measurements at baseline and each follow-up point. Generalized estimating equations were used to analyze the effects of baseline work stress on HRV over the following 1 year. Results: After adjusting for baseline characteristics and clinical data, anxiety, depression, and burnout scores, high JS was not associated with any HRV measures during follow-up (all p > 0.10), whereas high ERI was significantly related to slower recovery of 5 frequency domain HRV measures (TP, HF, LF, VLF, and ULF) (all p < 0.001), and marginally associated with one time domain measure (SDNN) (p = 0.069). When mutually adjusting for both work stress models, results of ERI remained nearly unchanged. Conclusion: Work stress in terms of ERI predicted lower HRV during the one-year period after ACS, especially frequency domain measures.